Detailed results of CTR148A_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 >>>----------+
| |
| CTR148A_XRay_em_bcr3_noHs_000.rin 0.0 150 residues |
| |
| Ramachandran plot: 91.9% core 8.1% allow 0.0% gener 0.0% disall |
| |
| All Ramachandrans: 0 labelled residues (out of 134) |
| Chi1-chi2 plots: 0 labelled residues (out of 92) |
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
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
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
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
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
654 -0.60
655 0.13
656 -0.18
657 -0.76
658 -0.53
659 -0.12
660 -0.43
661 0.31
662 0.38
663 -0.27
664 -0.31
665 -0.81
666 -1.27
667 -0.33
671 1.39
672 1.04
673 0.69
674 0.87
675 1.25
676 0.98
677 1.01
678 1.09
679 -0.27
680 -0.39
681 -1.63
682 -0.81
683 0.10
684 -0.25
685 -2.51
686 -0.23
687 -0.21
688 -1.13
689 -0.17
690 -1.38
691 -0.84
692 -1.41
693 -0.91
694 1.00
695 -0.78
696 0.20
697 0.30
698 -0.56
699 -0.01
703 -0.04
704 -0.01
705 0.29
706 -0.69
707 1.24
708 1.14
709 1.08
710 0.82
711 0.84
712 0.87
716 1.22
717 0.84
718 0.28
719 -0.26
720 -0.76
721 -0.41
722 -0.45
723 -0.37
724 -1.75
725 0.06
726 -1.23
727 -0.43
728 -0.35
729 -0.37
730 -0.33
743 -0.03
744 0.26
745 -0.15
746 -0.53
747 -0.53
748 -0.12
749 -0.43
750 0.31
751 0.31
752 -0.01
753 -0.45
754 -0.51
755 -0.25
756 0.29
760 1.39
761 1.04
762 1.01
763 0.87
764 1.02
765 0.98
766 1.01
767 0.88
768 0.37
769 -0.23
770 -0.51
771 -0.81
772 -0.14
773 -0.84
774 -2.09
775 -0.81
776 -0.21
777 -2.07
778 -0.17
779 -1.38
780 -1.78
781 -0.30
782 -0.41
783 1.03
784 0.31
785 0.01
786 -0.01
787 -0.75
788 -0.11
792 -0.04
793 -0.19
794 0.85
795 -0.33
796 0.87
797 1.32
798 1.08
799 0.99
800 0.77
801 1.24
805 1.22
806 0.85
807 0.33
808 -0.26
809 -0.48
810 -0.53
811 0.25
812 -0.48
813 -2.36
814 0.06
815 -0.40
816 -0.35
817 -0.35
#Reported_Model_Average -0.057
#Overall_Average_Reported -0.057
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
653 0.00
654 -0.20
655 0.03
656 0.07
657 -0.76
658 -0.53
659 0.38
660 -0.10
661 -0.74
662 0.26
663 -0.27
664 -0.33
665 -0.65
666 -0.08
667 -0.48
668 0.00
670 -0.29
671 -0.16
672 0.22
673 -0.15
674 0.88
675 1.25
676 0.63
677 0.96
678 0.19
679 0.44
680 -0.82
681 -1.27
682 -0.09
683 0.09
684 0.29
685 -2.68
686 0.03
687 0.35
688 -0.49
689 -0.73
690 -1.63
691 -0.84
692 -0.85
693 0.02
694 1.00
695 -0.50
696 -0.35
697 0.30
698 -0.22
699 0.52
700 -0.15
702 0.10
703 -0.34
704 -0.55
705 0.52
706 -0.43
707 0.94
708 1.16
709 0.41
710 0.67
711 0.28
712 0.68
713 0.53
715 1.13
716 0.36
717 0.41
718 0.11
719 0.43
720 0.05
721 0.04
722 -0.45
723 0.39
724 -1.13
725 0.27
726 -0.32
727 -0.78
728 0.18
729 0.10
730 0.44
731 0.00
742 0.00
743 -0.55
744 0.19
745 0.05
746 -0.53
747 -0.53
748 0.38
749 -0.10
750 -0.46
751 0.56
752 -0.01
753 -0.59
754 -0.51
755 -0.25
756 0.29
757 0.00
759 0.29
760 1.09
761 0.12
762 0.32
763 0.82
764 1.02
765 0.79
766 0.92
767 1.04
768 0.66
769 -0.66
770 -0.14
771 -0.84
772 -0.15
773 -0.01
774 -1.23
775 -0.84
776 0.35
777 -0.63
778 -0.69
779 -0.59
780 -1.78
781 -0.42
782 0.09
783 1.03
784 0.14
785 -0.31
786 0.23
787 -0.31
788 0.48
789 0.40
791 -0.21
792 -1.19
793 -0.63
794 0.54
795 -0.50
796 0.58
797 0.21
798 0.40
799 0.76
800 -0.05
801 0.47
802 0.34
804 -0.35
805 0.92
806 0.73
807 0.66
808 0.24
809 0.16
810 0.11
811 0.25
812 0.22
813 -1.57
814 -0.41
815 0.17
816 0.26
817 0.18
818 0.55
#Reported_Model_Average -0.002
#Overall_Average_Reported -0.002
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
653 0.00
654 0.51
655 0.71
656 -0.33
657 0.49
658 1.10
659 0.93
660 0.71
661 0.93
662 -0.74
663 1.10
664 -0.59
665 0.51
666 0.47
667 0.41
668 1.10
669 0.23
670 0.55
671 0.51
672 0.25
673 0.93
674 0.55
675 1.10
676 -0.09
677 0.93
678 0.59
679 -0.10
680 1.40
681 0.23
682 0.55
683 0.51
684 0.81
685 0.71
686 0.08
687 0.93
688 -0.74
689 1.06
690 0.51
691 0.49
692 -0.10
693 0.23
694 1.10
695 -0.94
696 1.40
697 0.08
698 1.29
699 -0.26
700 1.06
701 0.23
702 0.93
703 0.71
704 0.66
705 0.47
706 0.51
707 0.08
708 0.23
709 0.08
710 1.06
711 0.08
712 0.08
713 1.06
714 1.00
715 0.51
716 0.47
717 1.06
718 0.24
719 -0.10
720 -0.09
721 -0.03
722 1.10
723 0.66
724 -0.84
725 0.08
726 1.00
727 0.28
728 -0.88
729 -0.68
730 0.34
731 0.00
742 0.00
743 0.51
744 0.71
745 -0.33
746 0.49
747 1.10
748 0.93
749 0.24
750 0.93
751 -0.74
752 1.10
753 -0.59
754 0.51
755 0.00
756 0.00
757 1.10
758 1.00
759 0.55
760 0.51
761 0.25
762 0.93
763 0.55
764 1.10
765 -0.09
766 0.93
767 0.59
768 0.47
769 1.04
770 0.51
771 0.55
772 0.51
773 0.81
774 0.71
775 0.55
776 0.93
777 -0.74
778 1.06
779 0.51
780 -0.25
781 -0.10
782 0.23
783 1.10
784 -0.94
785 1.40
786 0.08
787 1.29
788 -0.26
789 1.06
790 -0.83
791 0.93
792 0.71
793 1.00
794 0.47
795 0.51
796 0.08
797 0.23
798 0.08
799 1.06
800 0.08
801 0.08
802 1.06
803 0.91
804 0.51
805 0.47
806 1.06
807 0.24
808 -0.10
809 0.66
810 -0.03
811 1.10
812 0.66
813 -0.84
814 0.08
815 1.00
816 0.04
817 -0.88
818 -0.68
#Reported_Model_Average 0.423
#Overall_Average_Reported 0.423
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
653 0.00
654 0.51
655 0.71
656 -0.33
657 0.49
658 1.10
659 0.93
660 0.71
661 0.93
662 -0.74
663 1.10
664 -0.59
665 0.51
666 0.47
667 0.41
668 1.10
669 0.23
670 0.55
671 0.51
672 0.25
673 0.93
674 0.55
675 1.10
676 -0.09
677 0.93
678 0.59
679 -0.10
680 1.40
681 0.23
682 0.55
683 0.51
684 0.81
685 0.71
686 0.08
687 0.93
688 -0.74
689 1.06
690 0.51
691 0.49
692 -0.10
693 0.23
694 1.10
695 -0.94
696 1.40
697 0.08
698 1.29
699 -0.26
700 1.06
701 0.23
702 0.93
703 0.71
704 0.66
705 0.47
706 0.51
707 0.08
708 0.23
709 0.08
710 1.06
711 0.08
712 0.08
713 1.06
714 1.00
715 0.51
716 0.47
717 1.06
718 0.24
719 -0.10
720 -0.09
721 -0.03
722 1.10
723 0.66
724 -0.84
725 0.08
726 1.00
727 0.28
728 -0.88
729 -0.68
730 0.34
731 0.00
742 0.00
743 0.51
744 0.71
745 -0.33
746 0.49
747 1.10
748 0.93
749 0.24
750 0.93
751 -0.74
752 1.10
753 -0.59
754 0.51
755 0.00
756 0.00
757 1.10
758 1.00
759 0.55
760 0.51
761 0.25
762 0.93
763 0.55
764 1.10
765 -0.09
766 0.93
767 0.59
768 0.47
769 1.04
770 0.51
771 0.55
772 0.51
773 0.81
774 0.71
775 0.55
776 0.93
777 -0.74
778 1.06
779 0.51
780 -0.25
781 -0.10
782 0.23
783 1.10
784 -0.94
785 1.40
786 0.08
787 1.29
788 -0.26
789 1.06
790 -0.83
791 0.93
792 0.71
793 1.00
794 0.47
795 0.51
796 0.08
797 0.23
798 0.08
799 1.06
800 0.08
801 0.08
802 1.06
803 0.91
804 0.51
805 0.47
806 1.06
807 0.24
808 -0.10
809 0.66
810 -0.03
811 1.10
812 0.66
813 -0.84
814 0.08
815 1.00
816 0.04
817 -0.88
818 -0.68
#Reported_Model_Average 0.423
#Overall_Average_Reported 0.423
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
653.000 0
654.000 0
655.000 0
656.000 1
657.000 0
658.000 0
659.000 0
660.000 0
661.000 0
662.000 0
663.000 0
664.000 0
665.000 0
666.000 0
667.000 0
668.000 0
669.000 0
670.000 0
671.000 2
672.000 0
673.000 2
674.000 0
675.000 0
676.000 0
677.000 0
678.000 0
679.000 0
680.000 0
681.000 0
682.000 0
683.000 1
684.000 1
685.000 7
686.000 0
687.000 0
688.000 0
689.000 0
690.000 0
691.000 0
692.000 0
693.000 0
694.000 0
695.000 0
696.000 0
697.000 0
698.000 0
699.000 0
700.000 1
701.000 1
702.000 1
703.000 5
704.000 0
705.000 0
706.000 0
707.000 0
708.000 1
709.000 0
710.000 0
711.000 0
712.000 1
713.000 0
714.000 0
715.000 0
716.000 0
717.000 0
718.000 0
719.000 0
720.000 0
721.000 0
722.000 0
723.000 0
724.000 0
725.000 0
726.000 0
727.000 0
728.000 0
729.000 0
730.000 1
731.000 1
732.000 0
733.000 0
734.000 0
735.000 0
736.000 0
737.000 0
738.000 0
739.000 0
740.000 0
741.000 0
742.000 0
743.000 0
744.000 0
745.000 3
746.000 0
747.000 0
748.000 0
749.000 0
750.000 0
751.000 0
752.000 0
753.000 0
754.000 0
755.000 0
756.000 0
757.000 0
758.000 0
759.000 0
760.000 0
761.000 0
762.000 0
763.000 0
764.000 0
765.000 0
766.000 1
767.000 0
768.000 0
769.000 2
770.000 0
771.000 3
772.000 1
773.000 4
774.000 2
775.000 0
776.000 0
777.000 0
778.000 0
779.000 0
780.000 0
781.000 0
782.000 0
783.000 0
784.000 0
785.000 0
786.000 0
787.000 0
788.000 0
789.000 2
790.000 3
791.000 3
792.000 5
793.000 1
794.000 0
795.000 0
796.000 0
797.000 0
798.000 0
799.000 0
800.000 4
801.000 0
802.000 0
803.000 4
804.000 0
805.000 0
806.000 0
807.000 0
808.000 0
809.000 0
810.000 0
811.000 0
812.000 0
813.000 0
814.000 0
815.000 0
816.000 0
817.000 0
818.000 0
#Reported_Model_Average 0.386
#Overall_Average_Reported 0.386
List of bad contacts calculated by MAGE
/farm/software/bin/probe
: 2464:M 685 ARG 2HD :M 703 PHE HD2 : -0.870: 37
: 2464:M 703 PHE CD2 :M 685 ARG 2HD : -0.753: 37
: 2464:M 703 PHE 1HB :M 683 ASN 2HB : -0.579: 27
: 2464:M 685 ARG CD :M 703 PHE CD2 : -0.541: 37
: 2464:M 684 ILE C :M 685 ARG 1HD : -0.457: 33
: 2464:M 685 ARG 2HG :M 703 PHE CE2 : -0.423: 34
: 2464:M 685 ARG N :M 685 ARG 1HD : -0.406: 33
: 2464:M 803 MET 2HE :M 800 THR HA : -0.852: 38
: 2464:M 803 MET CE :M 800 THR HA : -0.850: 38
: 2464:M 803 MET 2HE :M 800 THR CA : -0.549: 38
: 2464:M 803 MET CE :M 800 THR 2HG2 : -0.475: 38
: 2464:M 769 PHE HD2 :M 771 THR 3HG2 : -0.830: 35
: 2464:M 769 PHE CD2 :M 771 THR 3HG2 : -0.582: 35
: 2464:M 771 THR 2HG2 :M 793 VAL 2HG1 : -0.433: 35
: 2464:M 792 PHE 1HB :M 772 ASN 2HB : -0.802: 24
: 2464:M 792 PHE CZ :M 774 ARG 1HD : -0.462: 47
: 2464:M 792 PHE HD1 :M 792 PHE HA : -0.418: 40
: 2464:M 774 ARG 1HD :M 792 PHE CE2 : -0.403: 45
: 2464:M 773 ILE H :M 671 ASN 1HD2 : -0.625: 15
: 2464:M 789 LEU HG :M 791 ILE 3HG2 : -0.611: 21
: 2464:M 766 ILE 2HG2 :M 773 ILE 1HD1 : -0.609: 25
: 2464:M 773 ILE H :M 671 ASN ND2 : -0.476: 15
: 2464:M 791 ILE 2HG2 :M 773 ILE HA : -0.429: 16
: 2464:M 791 ILE 3HG2 :M 789 LEU CG : -0.400: 21
: 2464:M 745 LEU HG :M 790 MET CE : -0.608: 25
: 2464:M 745 LEU 1HD2 :M 790 MET 2HE : -0.537: 36
: 2464:M 790 MET CE :M 745 LEU CG : -0.430: 25
: 2464:M 708 ASP O :M 712 THR 3HG2 : -0.595: 20
: 2464:M 730 SER O :M 731 ASN CB : -0.576: 37
: 2464:M 701 MET CE :M 656 LEU HG : -0.526: 26
: 2464:M 702 ILE 3HG2 :M 700 LEU HG : -0.487: 20
: 2464:M 673 ILE 3HD1 :M 673 ILE HA : -0.410: 24
#sum2 ::12.99 clashscore : 12.36 clashscore B<40
#summary::2464 atoms:2346 atoms B<40:276304 potential dots:17270.0 A^2:32 bumps:29 bumps B<40:908.5 score
Output from PDB validation software
Summary from PDB validation
May. 10, 00:45:34 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 0.006 Angstroms
All covalent bonds lie within a 6.0*RMSD range about the
standard dictionary values.
*** Covalent Angle Values:
The RMS deviation for covalent angles relative to the standard
dictionary is 1.3 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
--------------------------------------------------------------------------------
-8.1 LYS A 666 CB - CA - C 102.0 110.1
7.9 ASN A 667 N - CA - C 119.1 111.2
-9.4 PHE A 703 N - CA - C 101.8 111.2
-8.8 VAL A 726 N - CA - C 102.4 111.2
7.9 ASN B 667 N - CA - C 119.1 111.2
-9.4 VAL B 688 N - CA - C 101.8 111.2
-8.7 PHE B 703 N - CA - C 102.5 111.2
-9.8 VAL B 726 N - CA - C 101.4 111.2
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.
==> The following residues have missing atoms:
RES MOD#C SEQ ATOMS
THR( A 653) OG1 CG2
ASN( A 731) CG OD1 ND2
THR( B 653) OG1 CG2
LYS( B 666) CG CD CE NZ
ASN( B 667) CG OD1 ND2
CTR148A_XRay_em_bcr3.pdb: Error: Z value is 16. It should be 8.