Detailed results of PFR193A_XRay_em_bcr3 by PSVS
Output from PDBStat
Output from PROCHECK
Ramachandran Plot for all models
Text summary of Ramachandran Plot
+----------<<< P R O C H E C K S U M M A R Y >>>----------+
| |
| PFR193A_XRay_em_bcr3_noHs_000.rin 0.0 224 residues |
| |
+| Ramachandran plot: 91.1% core 8.4% allow 0.5% gener 0.0% disall |
| |
+| All Ramachandrans: 1 labelled residues (out of 214) |
+| Chi1-chi2 plots: 1 labelled residues (out of 125) |
JPEG image for all model Ramachandran Plot
Residue Properties for all models
JPEG for all model Residue Properties - page $num_n
JPEG for all model Residue Properties - page $num_n
JPEG for all model Residue Properties - page $num_n
JPEG for all model Residue Properties - page $num_n
Model Secondary Structures from Procheck
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
JPEG for Model Secondary Structures - page $num_n
Ramachandran Plots for each residue
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
JPEG for residue Ramachandran Plots - page $num_n
Ramachandran analysis for each residue from Molprobity
Chi1-Chi2 Plots for each residue
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
JPEG for residue Chi1-Chi2 Plots - page $num_n
Procheck G-factors for phi-psi for each residue
JPEG image for residue phi-psi G-factors
Table of Procheck G-factors for phi-psi for ordered residues
#phipsi_gfactor
#Residue\Model average
424 -0.14
425 -0.56
426 -0.80
427 -1.22
428 -2.11
429 -1.35
430 -0.48
435 -2.54
436 -0.49
437 0.14
438 -1.94
439 -1.24
440 -0.15
441 0.16
442 -0.06
443 -0.87
444 0.26
445 -0.20
446 -0.57
447 0.40
448 0.34
449 -1.23
450 -0.05
451 -1.13
452 -1.80
453 0.45
454 -0.17
455 -0.50
456 -0.77
457 -0.62
458 0.09
459 -0.59
460 -0.05
461 -0.71
462 0.53
463 -0.32
464 -0.44
465 -0.41
466 -0.09
467 -0.35
468 0.31
469 -0.12
470 -2.07
471 0.62
472 -1.44
473 -0.57
474 -0.33
475 0.42
476 -0.10
477 0.42
478 0.60
479 -0.56
480 0.58
481 0.11
482 0.24
483 -0.65
484 -1.56
485 -0.30
486 -0.44
487 -0.49
488 -0.63
489 -0.41
490 -0.09
491 -1.48
492 -0.29
493 0.37
494 -1.02
495 -0.69
496 -0.43
497 -0.25
498 -0.05
499 -0.12
500 0.13
501 -0.97
502 -0.67
503 -1.57
504 -1.73
505 0.40
506 -0.66
507 -0.63
508 -1.69
512 -0.52
513 0.07
514 -0.33
515 -0.78
516 0.40
517 0.04
518 -0.41
519 0.87
520 -0.59
521 -1.15
522 0.12
523 0.39
524 -0.76
525 -1.85
526 0.21
527 -1.92
528 -0.77
529 0.52
530 -0.21
531 0.52
532 0.31
533 -0.90
534 0.34
535 -1.21
536 -0.63
537 0.38
538 -1.14
539 -0.27
552 -1.19
553 -0.39
554 -3.23
555 -0.32
556 0.19
557 -1.24
558 -0.31
559 -0.57
560 -0.33
561 -0.65
562 0.31
563 -0.28
564 -0.57
565 -0.72
566 0.29
567 -1.23
568 -0.35
569 -1.13
570 -0.78
571 0.25
572 -0.30
573 -0.28
574 -0.77
575 -0.59
576 0.09
577 -0.59
578 -0.05
579 -0.71
580 0.53
581 -0.34
582 -0.43
583 -0.46
584 -0.12
585 -0.08
586 -0.15
587 -0.28
588 -1.13
589 0.42
590 -1.44
591 -0.56
592 -0.33
593 0.42
594 -0.07
595 0.31
596 0.40
597 -0.56
598 0.58
599 0.67
600 0.24
601 -0.50
602 -2.07
603 -0.32
604 -0.33
605 -0.17
606 0.17
607 -0.06
608 0.02
609 -0.80
610 -0.06
611 0.62
612 -2.10
613 -0.35
614 -0.58
615 -0.23
616 0.23
617 -0.22
618 0.40
619 0.22
620 -0.65
621 -1.05
622 -1.73
623 0.37
624 -0.25
625 -0.30
626 -1.05
630 -0.52
631 0.28
632 -0.26
633 -0.78
634 0.40
635 0.04
636 -0.28
637 0.61
638 -0.59
639 -0.65
640 0.00
641 0.12
642 -0.48
643 -1.11
644 0.84
645 -1.15
646 -0.56
647 -0.05
648 -0.69
649 0.52
650 0.04
651 -0.76
652 -0.01
653 -1.68
654 -0.60
655 0.31
656 -0.76
657 0.31
658 -0.06
659 -1.44
#Reported_Model_Average -0.403
#Overall_Average_Reported -0.403
Procheck G-factors for all dihedral angles for each residue
JPEG image for residue all dihedral G-factors
Table of Procheck G-factors for all dihedrals for ordered residues
#alldih_gfactor
#Residue\Model average
423 -0.88
424 -1.17
425 -0.28
426 -0.35
427 -2.06
428 -0.89
429 -0.23
430 -0.75
431 -1.22
434 -0.29
435 -0.98
436 -0.25
437 0.35
438 -1.94
439 -0.43
440 0.20
441 -0.36
442 -0.15
443 -0.66
444 0.37
445 0.33
446 -0.57
447 0.40
448 -0.41
449 -0.37
450 -0.15
451 -1.13
452 -1.44
453 0.82
454 0.57
455 0.02
456 -0.77
457 0.25
458 0.31
459 -0.09
460 0.53
461 -1.11
462 -0.27
463 -0.23
464 -0.28
465 0.05
466 -0.09
467 -0.35
468 0.14
469 -0.12
470 -0.66
471 0.62
472 -1.08
473 -0.73
474 0.41
475 0.70
476 0.48
477 0.19
478 0.26
479 0.03
480 0.06
481 0.11
482 0.56
483 -0.16
484 -0.55
485 0.23
486 -0.45
487 -0.37
488 -0.76
489 -0.33
490 0.49
491 -0.44
492 -0.29
493 0.37
494 0.08
495 0.07
496 0.17
497 0.44
498 0.18
499 0.20
500 -0.08
501 -0.77
502 0.14
503 -1.25
504 -0.84
505 0.40
506 -0.01
507 -0.08
508 -1.22
509 0.00
511 0.53
512 0.05
513 -1.03
514 -0.16
515 -0.78
516 0.44
517 -0.52
518 -0.39
519 0.45
520 -0.58
521 -0.38
522 0.44
523 0.39
524 0.02
525 -1.22
526 0.54
527 -0.89
528 -0.68
529 0.45
530 -0.02
531 -0.59
532 0.40
533 -0.90
534 0.31
535 -1.03
536 0.03
537 0.48
538 -0.58
539 0.24
540 -0.25
551 0.05
552 -0.57
553 0.19
554 -1.67
555 -2.31
556 0.19
557 -0.70
558 -0.19
559 -0.73
560 -0.70
561 -0.41
562 0.59
563 -0.11
564 -0.57
565 -0.72
566 -0.27
567 -0.63
568 -0.72
569 -1.13
570 -0.93
571 0.78
572 -0.04
573 0.02
574 -0.77
575 0.10
576 0.22
577 0.02
578 0.23
579 -0.53
580 -0.27
581 -0.63
582 -0.37
583 0.02
584 -0.12
585 -0.08
586 -0.09
587 -0.28
588 -0.13
589 0.42
590 -1.08
591 -0.72
592 0.41
593 0.46
594 0.50
595 -0.38
596 0.41
597 -0.29
598 0.57
599 0.67
600 0.36
601 0.02
602 -0.82
603 -0.25
604 -0.64
605 -0.13
606 0.33
607 -0.04
608 0.54
609 -0.22
610 -0.06
611 0.62
612 -0.85
613 0.21
614 0.01
615 0.36
616 0.49
617 0.14
618 0.22
619 0.15
620 -0.06
621 -0.85
622 -0.63
623 0.37
624 0.26
625 -0.73
626 -1.94
627 0.00
629 0.23
630 -0.58
631 -0.99
632 -0.10
633 -0.78
634 0.34
635 -0.52
636 -0.32
637 -0.14
638 -0.58
639 -0.11
640 0.02
641 -0.48
642 0.13
643 -0.46
644 0.86
645 -0.51
646 -0.25
647 0.18
648 -0.36
649 -0.59
650 0.32
651 -0.76
652 0.38
653 -0.90
654 0.25
655 0.40
656 0.06
657 0.40
658 -0.31
659 -0.81
660 -0.34
#Reported_Model_Average -0.209
#Overall_Average_Reported -0.209
Output from Verify3D
Verify3D Score over a window of $winsize_s residues
JPEG image for Verify3D Score
Table of Verify3D scores for ordered residues across all models
#verify3d
#Residue\Model only_model
423 0.08
424 0.23
425 -0.43
426 0.51
427 -0.10
428 0.29
429 0.59
430 0.41
431 -1.14
434 0.08
435 -0.84
436 0.04
437 -0.84
438 0.64
439 0.34
440 1.06
441 0.55
442 0.66
443 -0.59
444 0.93
445 0.47
446 1.10
447 0.44
448 0.23
449 -0.74
450 0.66
451 1.10
452 -0.74
453 0.41
454 0.47
455 -0.68
456 0.49
457 0.28
458 0.52
459 0.28
460 1.00
461 1.04
462 1.00
463 0.08
464 -0.56
465 0.29
466 1.10
467 1.10
468 -0.94
469 1.10
470 1.00
471 0.25
472 0.34
473 0.55
474 0.47
475 1.00
476 0.71
477 1.00
478 1.25
479 0.93
480 0.51
481 1.10
482 0.08
483 -0.68
484 1.25
485 0.47
486 0.41
487 1.62
488 0.08
489 1.00
490 0.17
491 0.77
492 1.10
493 0.44
494 0.47
495 0.28
496 0.28
497 0.47
498 -0.74
499 1.06
500 0.08
501 1.40
502 0.51
503 0.96
504 0.08
505 -0.07
506 0.08
507 -0.03
508 0.28
509 1.10
510 -0.83
511 1.25
512 0.24
513 0.93
514 -0.26
515 0.49
516 0.55
517 1.00
518 -0.83
519 0.28
520 0.28
521 0.51
522 0.08
523 -0.09
524 -0.80
525 -0.46
526 -0.68
527 0.51
528 0.28
529 0.41
530 0.51
531 0.51
532 -0.74
533 0.49
534 0.08
535 0.71
536 0.51
537 1.00
538 0.59
539 1.00
540 -0.80
551 0.08
552 0.08
553 -1.63
554 0.28
555 -0.84
556 0.64
557 0.34
558 1.06
559 0.55
560 0.66
561 0.28
562 0.81
563 0.47
564 1.10
565 0.44
566 0.23
567 -0.74
568 -0.09
569 1.10
570 -0.40
571 0.51
572 0.47
573 -0.68
574 0.49
575 0.28
576 0.52
577 -0.59
578 1.00
579 1.04
580 1.00
581 0.08
582 -0.56
583 -0.68
584 1.10
585 1.10
586 -0.94
587 1.10
588 1.00
589 0.25
590 0.34
591 0.55
592 0.47
593 1.00
594 0.71
595 1.00
596 1.25
597 0.93
598 0.51
599 1.10
600 0.08
601 -0.68
602 1.25
603 0.47
604 0.51
605 1.62
606 0.08
607 1.00
608 0.17
609 0.77
610 1.10
611 0.44
612 0.47
613 0.28
614 -0.59
615 0.47
616 -0.74
617 1.06
618 0.08
619 1.40
620 0.51
621 0.96
622 0.08
623 -0.07
624 0.08
625 -0.03
626 -0.59
627 1.10
628 -0.83
629 1.25
630 0.24
631 0.93
632 -0.26
633 0.49
634 0.55
635 1.00
636 -0.83
637 0.28
638 0.28
639 0.51
640 0.08
641 -0.09
642 -0.80
643 -0.46
644 -0.33
645 0.51
646 0.28
647 0.41
648 0.51
649 0.51
650 -0.74
651 0.49
652 0.08
653 0.71
654 0.51
655 0.66
656 0.59
657 1.00
658 -0.74
659 -0.68
660 0.28
#Reported_Model_Average 0.341
#Overall_Average_Reported 0.341
Output from ProsaII
ProsaII Score over a window of $winsize_s residues
JPEG image for ProsaII Score
Table of Verify3D scores for ordered residues across all models
#verify3d
#Residue\Model only_model
423 0.08
424 0.23
425 -0.43
426 0.51
427 -0.10
428 0.29
429 0.59
430 0.41
431 -1.14
434 0.08
435 -0.84
436 0.04
437 -0.84
438 0.64
439 0.34
440 1.06
441 0.55
442 0.66
443 -0.59
444 0.93
445 0.47
446 1.10
447 0.44
448 0.23
449 -0.74
450 0.66
451 1.10
452 -0.74
453 0.41
454 0.47
455 -0.68
456 0.49
457 0.28
458 0.52
459 0.28
460 1.00
461 1.04
462 1.00
463 0.08
464 -0.56
465 0.29
466 1.10
467 1.10
468 -0.94
469 1.10
470 1.00
471 0.25
472 0.34
473 0.55
474 0.47
475 1.00
476 0.71
477 1.00
478 1.25
479 0.93
480 0.51
481 1.10
482 0.08
483 -0.68
484 1.25
485 0.47
486 0.41
487 1.62
488 0.08
489 1.00
490 0.17
491 0.77
492 1.10
493 0.44
494 0.47
495 0.28
496 0.28
497 0.47
498 -0.74
499 1.06
500 0.08
501 1.40
502 0.51
503 0.96
504 0.08
505 -0.07
506 0.08
507 -0.03
508 0.28
509 1.10
510 -0.83
511 1.25
512 0.24
513 0.93
514 -0.26
515 0.49
516 0.55
517 1.00
518 -0.83
519 0.28
520 0.28
521 0.51
522 0.08
523 -0.09
524 -0.80
525 -0.46
526 -0.68
527 0.51
528 0.28
529 0.41
530 0.51
531 0.51
532 -0.74
533 0.49
534 0.08
535 0.71
536 0.51
537 1.00
538 0.59
539 1.00
540 -0.80
551 0.08
552 0.08
553 -1.63
554 0.28
555 -0.84
556 0.64
557 0.34
558 1.06
559 0.55
560 0.66
561 0.28
562 0.81
563 0.47
564 1.10
565 0.44
566 0.23
567 -0.74
568 -0.09
569 1.10
570 -0.40
571 0.51
572 0.47
573 -0.68
574 0.49
575 0.28
576 0.52
577 -0.59
578 1.00
579 1.04
580 1.00
581 0.08
582 -0.56
583 -0.68
584 1.10
585 1.10
586 -0.94
587 1.10
588 1.00
589 0.25
590 0.34
591 0.55
592 0.47
593 1.00
594 0.71
595 1.00
596 1.25
597 0.93
598 0.51
599 1.10
600 0.08
601 -0.68
602 1.25
603 0.47
604 0.51
605 1.62
606 0.08
607 1.00
608 0.17
609 0.77
610 1.10
611 0.44
612 0.47
613 0.28
614 -0.59
615 0.47
616 -0.74
617 1.06
618 0.08
619 1.40
620 0.51
621 0.96
622 0.08
623 -0.07
624 0.08
625 -0.03
626 -0.59
627 1.10
628 -0.83
629 1.25
630 0.24
631 0.93
632 -0.26
633 0.49
634 0.55
635 1.00
636 -0.83
637 0.28
638 0.28
639 0.51
640 0.08
641 -0.09
642 -0.80
643 -0.46
644 -0.33
645 0.51
646 0.28
647 0.41
648 0.51
649 0.51
650 -0.74
651 0.49
652 0.08
653 0.71
654 0.51
655 0.66
656 0.59
657 1.00
658 -0.74
659 -0.68
660 0.28
#Reported_Model_Average 0.341
#Overall_Average_Reported 0.341
Output from MolProbity
VdW violations from MAGE
JPEG image for MAGE VdW violation
Table of MAGE VdW violations for ordered residues across all models
#mage_clash
#Residue\Model only_model
423.000 0
424.000 0
425.000 0
426.000 0
427.000 0
428.000 0
429.000 0
430.000 0
431.000 2
432.000 0
433.000 0
434.000 0
435.000 1
436.000 0
437.000 2
438.000 2
439.000 1
440.000 0
441.000 0
442.000 1
443.000 0
444.000 0
445.000 0
446.000 0
447.000 0
448.000 0
449.000 0
450.000 3
451.000 3
452.000 1
453.000 1
454.000 3
455.000 1
456.000 0
457.000 0
458.000 0
459.000 0
460.000 1
461.000 0
462.000 1
463.000 2
464.000 0
465.000 0
466.000 1
467.000 0
468.000 1
469.000 0
470.000 0
471.000 0
472.000 0
473.000 0
474.000 0
475.000 0
476.000 0
477.000 1
478.000 0
479.000 0
480.000 0
481.000 0
482.000 0
483.000 0
484.000 0
485.000 1
486.000 0
487.000 2
488.000 0
489.000 0
490.000 0
491.000 1
492.000 0
493.000 0
494.000 1
495.000 0
496.000 2
497.000 0
498.000 0
499.000 1
500.000 0
501.000 0
502.000 1
503.000 1
504.000 0
505.000 1
506.000 0
507.000 0
508.000 0
509.000 0
510.000 0
511.000 0
512.000 0
513.000 5
514.000 0
515.000 1
516.000 0
517.000 1
518.000 1
519.000 0
520.000 0
521.000 1
522.000 0
523.000 0
524.000 0
525.000 1
526.000 2
527.000 0
528.000 0
529.000 0
530.000 0
531.000 0
532.000 0
533.000 1
534.000 0
535.000 0
536.000 0
537.000 1
538.000 0
539.000 3
540.000 0
541.000 0
542.000 0
543.000 0
544.000 0
545.000 0
546.000 0
547.000 0
548.000 0
549.000 0
550.000 0
551.000 0
552.000 1
553.000 1
554.000 2
555.000 1
556.000 2
557.000 1
558.000 0
559.000 0
560.000 0
561.000 0
562.000 0
563.000 0
564.000 0
565.000 0
566.000 0
567.000 0
568.000 0
569.000 0
570.000 1
571.000 0
572.000 1
573.000 1
574.000 0
575.000 0
576.000 0
577.000 0
578.000 1
579.000 1
580.000 0
581.000 2
582.000 1
583.000 0
584.000 1
585.000 0
586.000 1
587.000 0
588.000 0
589.000 0
590.000 0
591.000 0
592.000 1
593.000 0
594.000 0
595.000 1
596.000 0
597.000 2
598.000 0
599.000 0
600.000 0
601.000 0
602.000 0
603.000 0
604.000 0
605.000 1
606.000 0
607.000 0
608.000 0
609.000 0
610.000 0
611.000 0
612.000 1
613.000 0
614.000 2
615.000 0
616.000 1
617.000 1
618.000 0
619.000 0
620.000 1
621.000 0
622.000 0
623.000 0
624.000 0
625.000 0
626.000 3
627.000 0
628.000 0
629.000 0
630.000 0
631.000 7
632.000 0
633.000 0
634.000 0
635.000 0
636.000 3
637.000 0
638.000 2
639.000 1
640.000 1
641.000 2
642.000 0
643.000 1
644.000 1
645.000 0
646.000 0
647.000 0
648.000 0
649.000 0
650.000 0
651.000 0
652.000 0
653.000 0
654.000 0
655.000 1
656.000 0
657.000 0
658.000 0
659.000 2
660.000 1
#Reported_Model_Average 0.462
#Overall_Average_Reported 0.462
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 3531:M 614 GLU 2HG :M 581 LYS 1HG : -1.015: 32
: 3531:M 581 LYS 1HG :M 614 GLU CG : -0.542: 32
: 3531:M 496 GLU 2HG :M 463 LYS 1HG : -0.765: 24
: 3531:M 496 GLU CG :M 463 LYS 1HG : -0.608: 24
: 3531:M 631 ILE 2HG1 :M 597 ILE CD1 : -0.722: 32
: 3531:M 631 ILE 2HG1 :M 597 ILE 2HD1 : -0.630: 32
: 3531:M 631 ILE 2HD1 :M 631 ILE N : -0.591: 31
: 3531:M 631 ILE 3HD1 :M 655 VAL 3HG2 : -0.469: 31
: 3531:M 631 ILE CD1 :M 631 ILE N : -0.441: 31
: 3531:M 437 PHE 1HB :M 526 LEU CD2 : -0.638: 22
: 3531:M 437 PHE 1HB :M 526 LEU 1HD2 : -0.407: 22
: 3531:M 592 LYS 1HD :M 638 GLU OE1 : -0.626: 44
: 3531:M 638 GLU CG :M 640 THR 3HG2 : -0.463: 31
: 3531:M 573 LEU 1HD1 :M 620 ASN 2HB : -0.615: 25
: 3531:M 451 GLY 2HA :M 454 LYS 1HD : -0.607: 43
: 3531:M 454 LYS 1HB :M 451 GLY O : -0.449: 36
: 3531:M 454 LYS 1HD :M 451 GLY CA : -0.418: 43
: 3531:M 513 ILE N :M 513 ILE 2HD1 : -0.596: 29
: 3531:M 537 VAL 3HG2 :M 513 ILE 3HD1 : -0.527: 29
: 3531:M 513 ILE N :M 513 ILE CD1 : -0.455: 29
: 3531:M 450 VAL CG2 :M 539 VAL 2HG2 : -0.566: 41
: 3531:M 450 VAL O :M 539 VAL HA : -0.474: 43
: 3531:M 450 VAL 3HG2 :M 539 VAL 2HG2 : -0.466: 41
: 3531:M 525 GLU 2HB :M 439 ASP HA : -0.565: 10
: 3531:M 552 THR 1HG2 :M 644 LEU 3HD1 : -0.564: 23
: 3531:M 555 PHE CD1 :M 556 PRO 1HD : -0.549: 31
: 3531:M 584 GLY 2HA :M 556 PRO HA : -0.538: 17
: 3531:M 452 VAL 2HG2 :M 453 ASN ND2 : -0.543: 41
: 3531:M 460 VAL HB :M 499 LEU 1HB : -0.528: 18
: 3531:M 431 LEU C :M 431 LEU 3HD2 : -0.528: 35
: 3531:M 595 VAL 3HG2 :M 605 TRP HZ3 : -0.516: 18
: 3531:M 660 GLU OE1 :M 572 LYS 2HE : -0.506: 49
: 3531:M 455 LEU 1HD1 :M 502 ASN 2HB : -0.494: 35
: 3531:M 491 LEU 1HD1 :M 462 VAL 2HG2 : -0.493: 14
: 3531:M 626 GLU CD :M 626 GLU H : -0.492: 52
: 3531:M 570 VAL 1HG1 :M 659 LEU 3HD2 : -0.491: 47
: 3531:M 659 LEU 1HD2 :M 626 GLU OE1 : -0.407: 50
: 3531:M 487 TRP HZ3 :M 477 VAL 3HG2 : -0.478: 16
: 3531:M 485 LYS 2HD :M 487 TRP CZ2 : -0.463: 14
: 3531:M 639 ASN HA :M 636 ASP OD2 : -0.474: 27
: 3531:M 636 ASP OD2 :M 641 VAL 3HG1 : -0.459: 32
: 3531:M 641 VAL 3HG1 :M 636 ASP CG : -0.432: 32
: 3531:M 612 LYS HA :M 582 ASN O : -0.471: 20
: 3531:M 435 PHE HE1 :M 494 LYS 2HE : -0.469: 47
: 3531:M 616 VAL 3HG1 :M 579 HIS CD2 : -0.465: 27
: 3531:M 533 ALA 3HB :M 515 ALA 3HB : -0.451: 14
: 3531:M 557 ASP HA :M 643 GLU 2HB : -0.442: 19
: 3531:M 466 GLY 2HA :M 438 PRO HA : -0.426: 15
: 3531:M 521 ASN HA :M 518 ASP OD2 : -0.426: 17
: 3531:M 468 ILE O :M 438 PRO 2HB : -0.419: 15
: 3531:M 505 PRO 2HD :M 503 TRP O : -0.424: 33
: 3531:M 586 ILE 1HD1 :M 554 GLU 2HB : -0.418: 29
: 3531:M 553 PHE O :M 554 GLU C : -0.407: 27
: 3531:M 578 VAL HB :M 617 LEU 1HB : -0.416: 11
: 3531:M 442 VAL 3HG1 :M 517 VAL CG1 : -0.403: 22
#sum2 ::15.58 clashscore : 13.21 clashscore B<40
#summary::3531 atoms:3256 atoms B<40:395319 potential dots:24710.0 A^2:55 bumps:43 bumps B<40:1032 score
Output from PDB validation software
Summary from PDB validation
May. 10, 15:09:59 2013
Greetings,
[ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ]
The following checks were made on :
-----------------------------------------
DISTANCES AND ANGLES
We have checked your intra and intermolecular distances and angles with the
procedures currently in place at PDB:
==> The following solvent molecules are further away than 3.5 Angstroms from
macromolecule atoms which are available for hydrogen bonding in the
asymmetric unit.
none
The coordinates for water molecules which could be translated back into
the asymmetric unit are listed. If you do not indicate otherwise we will
replace the solvent coordinates in the entry with the ones below:
none
==> Close contacts in same asymmetric unit. Distances smaller than 2.2
Angstroms are considered as close contacts.
none
==> Close contacts based on crystal symmetry. Distances smaller than 2.2
Angstroms are considered as close contacts.
none
==> Bond and angle checks are performed by first computing the average rms
error for all bonds and angles relative to standard values for nucleotide
units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous
Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric
Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc.
1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate
Bond and Angle Parameters for X-ray protein structure refinement, Acta
Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the
dictionary values by more than six times this computed rms error is
identified as an outlier.
*** Covalent Bond Lengths:
The RMS deviation for covalent bonds relative to the standard
dictionary is 0.005 Angstroms
The following table contains a list of the covalent bonds
greater than 6.0*RMSD.
Deviation Residue Chain Sequence AT1 - AT2 Bond Dictionary
Name ID Number Distance Value
------------------------------------------------------------------------
0.039 VAL B 523 CA - CB 1.579 1.540
*** Covalent Angle Values:
The RMS deviation for covalent angles relative to the standard
dictionary is 1.2 degrees.
The following table contains a list of the covalent bond angles
greater than 6.0*RMSD.
Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary
Name ID Number Angle Value
--------------------------------------------------------------------------------
-8.5 ASN A 464 N - CA - C 102.7 111.2
-7.2 ILE A 479 N - CA - C 104.0 111.2
-9.8 THR A 488 N - CA - C 101.4 111.2
-7.9 VAL B 460 N - CA - C 103.3 111.2
-8.5 ILE B 479 N - CA - C 102.7 111.2
-11.6 THR B 488 N - CA - C 99.6 111.2
TORSION ANGLES
The torsion angle distributions have been checked. The postscript file of the
conformation rings showing the torsion angle distributions will be sent in a
separate E-mail message.
CHIRALITY
The chirality has been checked and there are no incorrect carbon chiral centers.
Some of O1P and O2P atoms do not follow the convention defined in the standard
IUBMB nomenclature (Liebecq, C. Compendium of Biochemical Nomenclature and Related
Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992). If you do not
indicate otherwise, we will switch the labels of O1P and O2P as shown below.
OTHER IMPORTANT ISSUES
==> Please check carefully REMARKS 3 and 200 and fill in the parameters as
appropriate.
SEQUENCE WARNING: Residue (A LEU 431 ) and Residue (A THR 434 ) are not linked
Distance of C-N bond is 6.06
PFR193A_XRay_em_bcr3.pdb: Error: Z value is 4. It should be 2.
PFR193A_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: A SSEQ: 33) in Token 'SITE' can not be found in coordinates
PFR193A_XRay_em_bcr3.pdb: Error: Record (RES: HOH CHNID: B SSEQ: 91) in Token 'SITE' can not be found in coordinates