Starting phenix.real_space_refine on Thu Feb 5 14:39:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1w_61982/02_2026/9k1w_61982.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1w_61982/02_2026/9k1w_61982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1w_61982/02_2026/9k1w_61982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1w_61982/02_2026/9k1w_61982.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1w_61982/02_2026/9k1w_61982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1w_61982/02_2026/9k1w_61982.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 34 5.49 5 S 102 5.16 5 C 11124 2.51 5 N 3031 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17679 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 6422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6422 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 34, 'TRANS': 773} Chain: "D" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "A" Number of atoms: 9158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9158 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 60, 'TRANS': 1107} Chain breaks: 5 Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 584 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 461 Classifications: {'RNA': 22} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 4, 'rna3p': 17} Chain: "H" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6591 SG CYS D 23 91.957 58.732 41.908 1.00 36.05 S ATOM 6615 SG CYS D 26 89.230 56.347 43.060 1.00 37.82 S ATOM 6862 SG CYS D 58 90.891 58.120 45.746 1.00 30.78 S ATOM 6883 SG CYS D 61 93.070 55.799 43.866 1.00 30.12 S ATOM 6504 SG CYS D 11 92.231 53.752 60.570 1.00 27.30 S ATOM 6767 SG CYS D 46 91.871 57.551 61.567 1.00 27.18 S ATOM 6790 SG CYS D 49 93.384 56.568 58.288 1.00 34.69 S ATOM 7061 SG CYS D 85 89.643 55.871 59.025 1.00 24.43 S ATOM 6642 SG CYS D 30 79.484 52.823 48.658 1.00 32.28 S ATOM 6663 SG CYS D 33 77.529 49.493 49.082 1.00 29.48 S ATOM 6958 SG CYS D 72 75.703 52.782 48.701 1.00 22.88 S ATOM 6982 SG CYS D 75 77.572 51.986 51.888 1.00 23.99 S Time building chain proxies: 3.93, per 1000 atoms: 0.22 Number of scatterers: 17679 At special positions: 0 Unit cell: (144.1, 129.8, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 102 16.00 P 34 15.00 O 3385 8.00 N 3031 7.00 C 11124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 805.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 23 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 49 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 11 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 46 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 30 " Number of angles added : 18 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 30 sheets defined 39.2% alpha, 18.0% beta 9 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'C' and resid 497 through 506 Processing helix chain 'C' and resid 508 through 516 Processing helix chain 'C' and resid 517 through 520 Processing helix chain 'C' and resid 522 through 527 removed outlier: 4.120A pdb=" N PHE C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 560 removed outlier: 3.785A pdb=" N HIS C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 551 " --> pdb=" O GLN C 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP C 557 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 558 " --> pdb=" O LYS C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 563 No H-bonds generated for 'chain 'C' and resid 561 through 563' Processing helix chain 'C' and resid 570 through 576 Processing helix chain 'C' and resid 580 through 584 removed outlier: 3.571A pdb=" N ILE C 583 " --> pdb=" O PRO C 580 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP C 584 " --> pdb=" O LEU C 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 580 through 584' Processing helix chain 'C' and resid 586 through 603 removed outlier: 3.585A pdb=" N ARG C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 591 " --> pdb=" O TYR C 587 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 614 removed outlier: 3.725A pdb=" N MET C 609 " --> pdb=" O GLY C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 621 through 638 removed outlier: 4.289A pdb=" N ALA C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA C 638 " --> pdb=" O VAL C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 643 No H-bonds generated for 'chain 'C' and resid 641 through 643' Processing helix chain 'C' and resid 644 through 652 removed outlier: 4.162A pdb=" N ALA C 650 " --> pdb=" O PRO C 646 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 651 " --> pdb=" O PHE C 647 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 676 removed outlier: 4.363A pdb=" N ARG C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY C 676 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 682 Proline residue: C 681 - end of helix Processing helix chain 'C' and resid 683 through 691 removed outlier: 3.646A pdb=" N GLU C 688 " --> pdb=" O ARG C 684 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.926A pdb=" N VAL C 695 " --> pdb=" O HIS C 692 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 696 " --> pdb=" O GLY C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 692 through 696' Processing helix chain 'C' and resid 701 through 716 Processing helix chain 'C' and resid 727 through 733 Processing helix chain 'C' and resid 740 through 757 removed outlier: 3.796A pdb=" N ALA C 744 " --> pdb=" O GLY C 740 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 745 " --> pdb=" O LYS C 741 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR C 752 " --> pdb=" O LYS C 748 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 754 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Proline residue: C 755 - end of helix Processing helix chain 'C' and resid 760 through 776 removed outlier: 4.062A pdb=" N ARG C 767 " --> pdb=" O ASN C 763 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU C 768 " --> pdb=" O TYR C 764 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 769 " --> pdb=" O TYR C 765 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 797 removed outlier: 3.642A pdb=" N ILE C 787 " --> pdb=" O GLU C 783 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 789 " --> pdb=" O LYS C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 810 Processing helix chain 'C' and resid 810 through 818 removed outlier: 3.948A pdb=" N LYS C 816 " --> pdb=" O PRO C 812 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS C 817 " --> pdb=" O PRO C 813 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 825 Processing helix chain 'C' and resid 826 through 845 removed outlier: 4.187A pdb=" N VAL C 838 " --> pdb=" O VAL C 834 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU C 839 " --> pdb=" O ASP C 835 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 840 " --> pdb=" O THR C 836 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 841 " --> pdb=" O THR C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 855 removed outlier: 3.901A pdb=" N ILE C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP C 855 " --> pdb=" O SER C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 879 removed outlier: 3.836A pdb=" N ARG C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 870 " --> pdb=" O LYS C 866 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 871 " --> pdb=" O MET C 867 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 879 " --> pdb=" O ILE C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 885 through 902 Processing helix chain 'C' and resid 909 through 922 Processing helix chain 'C' and resid 923 through 927 removed outlier: 3.985A pdb=" N LYS C 926 " --> pdb=" O LYS C 923 " (cutoff:3.500A) Proline residue: C 927 - end of helix No H-bonds generated for 'chain 'C' and resid 923 through 927' Processing helix chain 'C' and resid 928 through 941 Processing helix chain 'C' and resid 947 through 965 removed outlier: 5.080A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET C 962 " --> pdb=" O THR C 958 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C 963 " --> pdb=" O ALA C 959 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 980 removed outlier: 4.241A pdb=" N GLU C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 984 Processing helix chain 'C' and resid 986 through 1004 Processing helix chain 'C' and resid 1005 through 1009 removed outlier: 3.688A pdb=" N LYS C1008 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET C1009 " --> pdb=" O MET C1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1005 through 1009' Processing helix chain 'C' and resid 1012 through 1015 Processing helix chain 'C' and resid 1016 through 1021 Processing helix chain 'C' and resid 1022 through 1024 No H-bonds generated for 'chain 'C' and resid 1022 through 1024' Processing helix chain 'C' and resid 1028 through 1046 removed outlier: 3.647A pdb=" N GLN C1032 " --> pdb=" O HIS C1028 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP C1037 " --> pdb=" O GLU C1033 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C1038 " --> pdb=" O ASN C1034 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C1045 " --> pdb=" O ARG C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1063 removed outlier: 3.641A pdb=" N ILE C1058 " --> pdb=" O GLU C1054 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C1063 " --> pdb=" O CYS C1059 " (cutoff:3.500A) Processing helix chain 'C' and resid 1064 through 1068 removed outlier: 3.652A pdb=" N LYS C1067 " --> pdb=" O GLU C1064 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C1068 " --> pdb=" O LEU C1065 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1064 through 1068' Processing helix chain 'C' and resid 1070 through 1089 removed outlier: 3.757A pdb=" N ARG C1074 " --> pdb=" O LYS C1070 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN C1079 " --> pdb=" O ARG C1075 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C1081 " --> pdb=" O THR C1077 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C1082 " --> pdb=" O VAL C1078 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C1086 " --> pdb=" O GLY C1082 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA C1087 " --> pdb=" O TYR C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1100 removed outlier: 3.522A pdb=" N ASN C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1124 removed outlier: 3.813A pdb=" N CYS C1111 " --> pdb=" O GLN C1107 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C1123 " --> pdb=" O VAL C1119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1135 removed outlier: 3.631A pdb=" N GLU C1135 " --> pdb=" O ALA C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1159 removed outlier: 3.543A pdb=" N VAL C1147 " --> pdb=" O VAL C1143 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C1148 " --> pdb=" O GLN C1144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C1152 " --> pdb=" O LEU C1148 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 4.123A pdb=" N LYS C1163 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP C1164 " --> pdb=" O MET C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1165 through 1177 removed outlier: 3.969A pdb=" N VAL C1169 " --> pdb=" O TYR C1165 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR C1170 " --> pdb=" O ILE C1166 " (cutoff:3.500A) Proline residue: C1171 - end of helix removed outlier: 5.430A pdb=" N ASP C1175 " --> pdb=" O PRO C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1199 removed outlier: 3.842A pdb=" N ARG C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C1190 " --> pdb=" O GLN C1186 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C1199 " --> pdb=" O MET C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 3.977A pdb=" N LEU C1208 " --> pdb=" O CYS C1204 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS C1210 " --> pdb=" O ASP C1206 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C1213 " --> pdb=" O ASN C1209 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C1215 " --> pdb=" O LEU C1211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP C1216 " --> pdb=" O LEU C1212 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1220 removed outlier: 4.148A pdb=" N PHE C1220 " --> pdb=" O PRO C1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1220' Processing helix chain 'C' and resid 1223 through 1242 removed outlier: 3.704A pdb=" N VAL C1239 " --> pdb=" O GLU C1235 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C1240 " --> pdb=" O GLY C1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 3.711A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C1248 " --> pdb=" O CYS C1244 " (cutoff:3.500A) Processing helix chain 'C' and resid 1252 through 1254 No H-bonds generated for 'chain 'C' and resid 1252 through 1254' Processing helix chain 'C' and resid 1259 through 1275 removed outlier: 3.893A pdb=" N GLY C1275 " --> pdb=" O SER C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1281 Processing helix chain 'C' and resid 1297 through 1302 removed outlier: 4.033A pdb=" N TYR C1302 " --> pdb=" O GLU C1299 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 50 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.283A pdb=" N LYS D 104 " --> pdb=" O TYR D 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.516A pdb=" N ASN A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 4.269A pdb=" N ARG A 432 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.643A pdb=" N CYS A 624 " --> pdb=" O PRO A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 823 removed outlier: 3.846A pdb=" N ALA A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 821 " --> pdb=" O GLN A 817 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET A 823 " --> pdb=" O MET A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 removed outlier: 3.607A pdb=" N ALA A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1152 removed outlier: 3.912A pdb=" N ASP A1139 " --> pdb=" O HIS A1135 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE A1140 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1176 through 1181 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1186 through 1196 removed outlier: 4.227A pdb=" N GLU A1196 " --> pdb=" O ASN A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.572A pdb=" N LYS A1207 " --> pdb=" O GLU A1203 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1216 " --> pdb=" O ARG A1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 removed outlier: 3.700A pdb=" N LYS B 17 " --> pdb=" O HIS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.799A pdb=" N MET B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.502A pdb=" N LEU B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 19 removed outlier: 4.525A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 39 through 41 removed outlier: 6.058A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 6.493A pdb=" N THR A1120 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A1128 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 3 " --> pdb=" O ILE A1174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.704A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 54 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG A 42 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N THR A 52 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 62 through 69 removed outlier: 3.639A pdb=" N GLY A 81 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 78 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 89 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS A 103 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.803A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 208 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER A 225 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS A 219 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 234 removed outlier: 4.537A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 255 through 258 removed outlier: 3.567A pdb=" N ILE A 256 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 267 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.585A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 287 through 292 removed outlier: 6.931A pdb=" N GLN A 304 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 290 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 302 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 303 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 305 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 314 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A 325 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU A 316 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 287 through 292 removed outlier: 6.931A pdb=" N GLN A 304 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 290 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 302 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 303 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 305 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 310 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 336 through 342 removed outlier: 4.219A pdb=" N ALA A 338 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 350 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.777A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 777 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 445 through 450 removed outlier: 3.641A pdb=" N MET A 447 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 764 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL A 449 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 762 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 445 through 450 removed outlier: 3.641A pdb=" N MET A 447 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 764 " --> pdb=" O MET A 447 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL A 449 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A 762 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 761 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 456 through 460 removed outlier: 7.304A pdb=" N SER A 477 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 475 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 516 through 520 removed outlier: 3.697A pdb=" N GLN A 518 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG A 525 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 520 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 544 through 549 removed outlier: 3.717A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 557 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 556 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 564 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 587 through 591 removed outlier: 4.126A pdb=" N CYS A 589 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 591 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 606 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 637 through 643 removed outlier: 7.111A pdb=" N GLY A 668 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU A 640 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN A 666 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE A 642 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR A 664 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 700 through 706 removed outlier: 3.787A pdb=" N LYS A 700 " --> pdb=" O MET A 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 713 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU A 710 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER A 724 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 722 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 723 " --> pdb=" O HIS A 730 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS A 730 " --> pdb=" O TYR A 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 800 through 804 removed outlier: 3.610A pdb=" N ALA A 863 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER A 864 " --> pdb=" O GLN A 881 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN A 881 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 866 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 879 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 868 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 888 through 894 removed outlier: 6.489A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 891 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 906 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 893 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TYR A 904 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 905 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 941 " --> pdb=" O THR A 927 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 953 through 955 removed outlier: 3.607A pdb=" N VAL A 959 " --> pdb=" O TYR A 970 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU A 967 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 982 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 969 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 993 through 996 removed outlier: 3.807A pdb=" N ALA A1025 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LYS A1015 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU A1021 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A1087 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A1026 " --> pdb=" O GLN A1087 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1044 through 1045 removed outlier: 6.546A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5634 1.34 - 1.46: 2597 1.46 - 1.57: 9640 1.57 - 1.69: 68 1.69 - 1.81: 157 Bond restraints: 18096 Sorted by residual: bond pdb=" CB PRO A1131 " pdb=" CG PRO A1131 " ideal model delta sigma weight residual 1.492 1.608 -0.116 5.00e-02 4.00e+02 5.36e+00 bond pdb=" CB PRO C1257 " pdb=" CG PRO C1257 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.46e+00 bond pdb=" C THR C 717 " pdb=" N PRO C 718 " ideal model delta sigma weight residual 1.336 1.349 -0.013 9.80e-03 1.04e+04 1.84e+00 bond pdb=" CG PRO C1257 " pdb=" CD PRO C1257 " ideal model delta sigma weight residual 1.503 1.457 0.046 3.40e-02 8.65e+02 1.81e+00 bond pdb=" CA GLU C 691 " pdb=" C GLU C 691 " ideal model delta sigma weight residual 1.522 1.540 -0.018 1.41e-02 5.03e+03 1.54e+00 ... (remaining 18091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 24302 1.78 - 3.57: 308 3.57 - 5.35: 52 5.35 - 7.14: 10 7.14 - 8.92: 3 Bond angle restraints: 24675 Sorted by residual: angle pdb=" CA PRO A1131 " pdb=" N PRO A1131 " pdb=" CD PRO A1131 " ideal model delta sigma weight residual 112.00 106.44 5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" CA MET C 613 " pdb=" CB MET C 613 " pdb=" CG MET C 613 " ideal model delta sigma weight residual 114.10 120.78 -6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CA PRO C1257 " pdb=" N PRO C1257 " pdb=" CD PRO C1257 " ideal model delta sigma weight residual 112.00 107.39 4.61 1.40e+00 5.10e-01 1.09e+01 angle pdb=" C ASN A 932 " pdb=" N ASN A 933 " pdb=" CA ASN A 933 " ideal model delta sigma weight residual 121.54 127.78 -6.24 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N PRO A1131 " pdb=" CD PRO A1131 " pdb=" CG PRO A1131 " ideal model delta sigma weight residual 103.20 98.56 4.64 1.50e+00 4.44e-01 9.57e+00 ... (remaining 24670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 9781 16.93 - 33.86: 920 33.86 - 50.79: 214 50.79 - 67.72: 63 67.72 - 84.64: 35 Dihedral angle restraints: 11013 sinusoidal: 4764 harmonic: 6249 Sorted by residual: dihedral pdb=" CA GLU A 136 " pdb=" C GLU A 136 " pdb=" N LYS A 137 " pdb=" CA LYS A 137 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA PRO C1171 " pdb=" C PRO C1171 " pdb=" N LEU C1172 " pdb=" CA LEU C1172 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN A 933 " pdb=" C ASN A 933 " pdb=" N GLY A 934 " pdb=" CA GLY A 934 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 11010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1908 0.033 - 0.067: 620 0.067 - 0.100: 188 0.100 - 0.133: 110 0.133 - 0.167: 7 Chirality restraints: 2833 Sorted by residual: chirality pdb=" CA ASN A 933 " pdb=" N ASN A 933 " pdb=" C ASN A 933 " pdb=" CB ASN A 933 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CB VAL C 925 " pdb=" CA VAL C 925 " pdb=" CG1 VAL C 925 " pdb=" CG2 VAL C 925 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CB ILE C 641 " pdb=" CA ILE C 641 " pdb=" CG1 ILE C 641 " pdb=" CG2 ILE C 641 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 2830 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C1256 " -0.039 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO C1257 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C1257 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1257 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 390 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 391 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G H 3 " -0.021 2.00e-02 2.50e+03 9.28e-03 2.58e+00 pdb=" N9 G H 3 " 0.022 2.00e-02 2.50e+03 pdb=" C8 G H 3 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G H 3 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G H 3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G H 3 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G H 3 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G H 3 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G H 3 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G H 3 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G H 3 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G H 3 " 0.007 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3096 2.77 - 3.31: 15921 3.31 - 3.84: 27152 3.84 - 4.37: 30513 4.37 - 4.90: 54434 Nonbonded interactions: 131116 Sorted by model distance: nonbonded pdb=" O SER A 450 " pdb=" OG1 THR A 761 " model vdw 2.242 3.040 nonbonded pdb=" O GLY A 354 " pdb=" OG SER A 403 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR C 979 " pdb=" O ASP C1015 " model vdw 2.299 3.040 nonbonded pdb=" O ASN C1026 " pdb=" NE2 GLN C1032 " model vdw 2.305 3.120 nonbonded pdb=" NH1 ARG C1262 " pdb=" O ALA B 24 " model vdw 2.307 3.120 ... (remaining 131111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.110 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.116 18108 Z= 0.101 Angle : 0.536 10.114 24693 Z= 0.277 Chirality : 0.041 0.167 2833 Planarity : 0.003 0.057 3058 Dihedral : 14.979 84.644 6987 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 2132 helix: 0.58 (0.22), residues: 667 sheet: -0.74 (0.26), residues: 424 loop : -1.81 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 957 TYR 0.014 0.001 TYR C 587 PHE 0.016 0.001 PHE C1202 TRP 0.006 0.001 TRP C 819 HIS 0.005 0.000 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00221 (18096) covalent geometry : angle 0.52282 (24675) hydrogen bonds : bond 0.21751 ( 601) hydrogen bonds : angle 7.49842 ( 1666) metal coordination : bond 0.00258 ( 12) metal coordination : angle 4.39094 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.502 Fit side-chains REVERT: C 784 MET cc_start: 0.7639 (tmm) cc_final: 0.7327 (tmm) REVERT: A 298 MET cc_start: 0.7319 (ppp) cc_final: 0.7097 (ptt) REVERT: A 981 CYS cc_start: 0.6592 (t) cc_final: 0.6347 (t) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1196 time to fit residues: 45.5319 Evaluate side-chains 196 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 626 ASN C1079 ASN C1099 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN A 795 ASN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.186442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.141589 restraints weight = 23770.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.138736 restraints weight = 22009.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140879 restraints weight = 20200.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140715 restraints weight = 13371.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140888 restraints weight = 12316.126| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18108 Z= 0.164 Angle : 0.601 8.937 24693 Z= 0.301 Chirality : 0.044 0.165 2833 Planarity : 0.004 0.042 3058 Dihedral : 11.198 83.638 2860 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.18 % Allowed : 7.86 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2132 helix: 0.40 (0.21), residues: 679 sheet: -0.90 (0.25), residues: 450 loop : -1.98 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 957 TYR 0.014 0.001 TYR C1273 PHE 0.016 0.001 PHE B 47 TRP 0.010 0.001 TRP B 29 HIS 0.006 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00386 (18096) covalent geometry : angle 0.58492 (24675) hydrogen bonds : bond 0.04772 ( 601) hydrogen bonds : angle 5.52786 ( 1666) metal coordination : bond 0.01353 ( 12) metal coordination : angle 5.09850 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.588 Fit side-chains REVERT: C 784 MET cc_start: 0.7777 (tmm) cc_final: 0.7461 (tmm) REVERT: C 923 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6147 (pttt) REVERT: C 1060 PHE cc_start: 0.7808 (m-80) cc_final: 0.7600 (m-80) REVERT: A 326 ARG cc_start: 0.7334 (mtm180) cc_final: 0.7031 (mtm180) REVERT: A 583 MET cc_start: 0.0667 (mmt) cc_final: 0.0379 (mmt) REVERT: A 590 MET cc_start: 0.0575 (mmp) cc_final: -0.0580 (ttp) REVERT: A 715 MET cc_start: 0.6734 (mpp) cc_final: 0.5182 (mpp) outliers start: 22 outliers final: 12 residues processed: 229 average time/residue: 0.1218 time to fit residues: 42.8411 Evaluate side-chains 206 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 626 ASN Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 871 THR Chi-restraints excluded: chain C residue 923 LYS Chi-restraints excluded: chain C residue 1023 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 44 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 533 ASN C 550 HIS A 203 ASN A 304 GLN A 670 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.182021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136337 restraints weight = 23924.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132753 restraints weight = 21962.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135415 restraints weight = 20756.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135058 restraints weight = 13411.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136206 restraints weight = 12381.762| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18108 Z= 0.199 Angle : 0.636 10.481 24693 Z= 0.317 Chirality : 0.045 0.197 2833 Planarity : 0.004 0.044 3058 Dihedral : 11.214 83.875 2860 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.40 % Allowed : 12.54 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.18), residues: 2132 helix: 0.17 (0.21), residues: 675 sheet: -1.16 (0.25), residues: 457 loop : -2.13 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 957 TYR 0.025 0.002 TYR A1215 PHE 0.023 0.002 PHE A 955 TRP 0.012 0.002 TRP C1216 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00482 (18096) covalent geometry : angle 0.61570 (24675) hydrogen bonds : bond 0.05299 ( 601) hydrogen bonds : angle 5.35882 ( 1666) metal coordination : bond 0.01095 ( 12) metal coordination : angle 5.99531 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: C 550 HIS cc_start: 0.6521 (t70) cc_final: 0.6240 (t-170) REVERT: C 732 TRP cc_start: 0.7194 (OUTLIER) cc_final: 0.6883 (m-90) REVERT: C 784 MET cc_start: 0.7687 (tmm) cc_final: 0.7193 (tmm) REVERT: C 1060 PHE cc_start: 0.7978 (m-80) cc_final: 0.7681 (m-80) REVERT: C 1071 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7936 (ttpp) REVERT: A 186 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6440 (mt-10) REVERT: A 590 MET cc_start: 0.0891 (mmp) cc_final: -0.0274 (ptm) outliers start: 26 outliers final: 17 residues processed: 231 average time/residue: 0.1163 time to fit residues: 41.4688 Evaluate side-chains 215 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 732 TRP Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 871 THR Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 81 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 208 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1069 HIS A 203 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.185584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140645 restraints weight = 23795.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.137177 restraints weight = 22414.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139604 restraints weight = 21253.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139346 restraints weight = 13560.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140479 restraints weight = 12221.817| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18108 Z= 0.104 Angle : 0.533 8.741 24693 Z= 0.268 Chirality : 0.042 0.154 2833 Planarity : 0.004 0.044 3058 Dihedral : 11.047 86.224 2860 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.67 % Allowed : 14.59 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.18), residues: 2132 helix: 0.46 (0.21), residues: 673 sheet: -0.95 (0.25), residues: 464 loop : -2.14 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 767 TYR 0.012 0.001 TYR C 979 PHE 0.010 0.001 PHE A 788 TRP 0.011 0.001 TRP B 29 HIS 0.004 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00234 (18096) covalent geometry : angle 0.52205 (24675) hydrogen bonds : bond 0.03745 ( 601) hydrogen bonds : angle 4.93446 ( 1666) metal coordination : bond 0.00444 ( 12) metal coordination : angle 4.01222 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: C 675 MET cc_start: 0.7772 (tpp) cc_final: 0.7388 (mmm) REVERT: C 732 TRP cc_start: 0.7203 (OUTLIER) cc_final: 0.6988 (m-90) REVERT: C 1060 PHE cc_start: 0.7946 (m-80) cc_final: 0.7659 (m-80) REVERT: A 98 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7264 (ppp) REVERT: A 590 MET cc_start: 0.0486 (mmp) cc_final: -0.0464 (ptm) REVERT: A 715 MET cc_start: 0.6897 (mpp) cc_final: 0.5510 (mpp) REVERT: A 817 GLN cc_start: 0.7136 (mt0) cc_final: 0.6458 (tt0) REVERT: A 823 MET cc_start: 0.7298 (ppp) cc_final: 0.6972 (ppp) outliers start: 31 outliers final: 16 residues processed: 231 average time/residue: 0.1145 time to fit residues: 41.1254 Evaluate side-chains 217 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 732 TRP Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 203 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 210 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.183822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139191 restraints weight = 23776.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135383 restraints weight = 22292.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137980 restraints weight = 21042.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137623 restraints weight = 13451.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138456 restraints weight = 12177.481| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18108 Z= 0.137 Angle : 0.561 9.325 24693 Z= 0.280 Chirality : 0.043 0.164 2833 Planarity : 0.004 0.043 3058 Dihedral : 11.023 86.092 2860 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.72 % Allowed : 15.98 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.18), residues: 2132 helix: 0.42 (0.21), residues: 674 sheet: -1.00 (0.24), residues: 472 loop : -2.15 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.014 0.001 TYR C1273 PHE 0.013 0.001 PHE A 788 TRP 0.009 0.001 TRP C1216 HIS 0.005 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00329 (18096) covalent geometry : angle 0.54883 (24675) hydrogen bonds : bond 0.04099 ( 601) hydrogen bonds : angle 4.91596 ( 1666) metal coordination : bond 0.00624 ( 12) metal coordination : angle 4.39718 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.7847 (tpp) cc_final: 0.7606 (mmt) REVERT: C 1060 PHE cc_start: 0.7997 (m-80) cc_final: 0.7688 (m-80) REVERT: A 98 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7253 (ppp) REVERT: A 590 MET cc_start: 0.0854 (mmp) cc_final: -0.0094 (ptm) REVERT: A 715 MET cc_start: 0.6959 (mpp) cc_final: 0.5810 (mpp) REVERT: A 823 MET cc_start: 0.7292 (ppp) cc_final: 0.6884 (ppp) outliers start: 32 outliers final: 21 residues processed: 225 average time/residue: 0.1216 time to fit residues: 42.1165 Evaluate side-chains 218 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1195 MET Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 200 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.186006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141230 restraints weight = 23642.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137254 restraints weight = 21896.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138901 restraints weight = 20356.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139486 restraints weight = 13514.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.139680 restraints weight = 12421.756| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18108 Z= 0.103 Angle : 0.529 8.505 24693 Z= 0.265 Chirality : 0.042 0.150 2833 Planarity : 0.004 0.047 3058 Dihedral : 10.933 88.128 2860 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.56 % Allowed : 16.52 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.18), residues: 2132 helix: 0.53 (0.21), residues: 671 sheet: -0.87 (0.24), residues: 468 loop : -2.10 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.011 0.001 TYR C1273 PHE 0.010 0.001 PHE A 788 TRP 0.010 0.001 TRP B 29 HIS 0.004 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00233 (18096) covalent geometry : angle 0.51971 (24675) hydrogen bonds : bond 0.03536 ( 601) hydrogen bonds : angle 4.75930 ( 1666) metal coordination : bond 0.00412 ( 12) metal coordination : angle 3.68677 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.7814 (tpp) cc_final: 0.7563 (mmt) REVERT: C 923 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.5969 (pttt) REVERT: C 1060 PHE cc_start: 0.7982 (m-80) cc_final: 0.7664 (m-80) REVERT: D 95 LYS cc_start: 0.7306 (tttt) cc_final: 0.7101 (tttt) REVERT: A 98 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7240 (ppp) REVERT: A 590 MET cc_start: 0.0642 (mmp) cc_final: -0.0139 (ptm) REVERT: A 715 MET cc_start: 0.7088 (mpp) cc_final: 0.6207 (mpp) REVERT: A 817 GLN cc_start: 0.7140 (mt0) cc_final: 0.6447 (tt0) REVERT: A 823 MET cc_start: 0.7396 (ppp) cc_final: 0.6923 (ppp) outliers start: 29 outliers final: 18 residues processed: 225 average time/residue: 0.1159 time to fit residues: 40.9095 Evaluate side-chains 220 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 923 LYS Chi-restraints excluded: chain C residue 967 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1195 MET Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 208 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 HIS C 626 ASN C1034 ASN A 670 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139143 restraints weight = 24005.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135050 restraints weight = 21934.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136713 restraints weight = 20656.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.137240 restraints weight = 13443.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137461 restraints weight = 12584.765| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18108 Z= 0.137 Angle : 0.563 9.404 24693 Z= 0.282 Chirality : 0.043 0.152 2833 Planarity : 0.004 0.050 3058 Dihedral : 10.911 87.224 2860 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.83 % Allowed : 17.38 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.18), residues: 2132 helix: 0.40 (0.21), residues: 672 sheet: -0.97 (0.24), residues: 469 loop : -2.19 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.024 0.001 TYR C 898 PHE 0.013 0.001 PHE A 955 TRP 0.009 0.001 TRP C1216 HIS 0.007 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00329 (18096) covalent geometry : angle 0.55038 (24675) hydrogen bonds : bond 0.04112 ( 601) hydrogen bonds : angle 4.80582 ( 1666) metal coordination : bond 0.00546 ( 12) metal coordination : angle 4.45280 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 609 MET cc_start: 0.5952 (ptp) cc_final: 0.5670 (pmm) REVERT: C 675 MET cc_start: 0.7951 (tpp) cc_final: 0.7669 (mmt) REVERT: C 784 MET cc_start: 0.7754 (tmm) cc_final: 0.7509 (tmm) REVERT: C 923 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.5984 (pttt) REVERT: C 1060 PHE cc_start: 0.8115 (m-80) cc_final: 0.7807 (m-80) REVERT: D 95 LYS cc_start: 0.7315 (tttt) cc_final: 0.7104 (tttt) REVERT: A 98 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7230 (ppp) REVERT: A 590 MET cc_start: 0.0692 (mmp) cc_final: -0.0078 (ptm) REVERT: A 715 MET cc_start: 0.6982 (mpp) cc_final: 0.6351 (mpp) REVERT: A 823 MET cc_start: 0.7293 (ppp) cc_final: 0.6677 (ppp) outliers start: 34 outliers final: 25 residues processed: 227 average time/residue: 0.1094 time to fit residues: 39.4781 Evaluate side-chains 222 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 923 LYS Chi-restraints excluded: chain C residue 967 GLU Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1195 MET Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1061 ASN Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 189 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 194 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.184787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.140413 restraints weight = 23700.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.136541 restraints weight = 22969.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138158 restraints weight = 20356.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138678 restraints weight = 13745.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138820 restraints weight = 12822.735| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18108 Z= 0.113 Angle : 0.544 8.988 24693 Z= 0.272 Chirality : 0.042 0.161 2833 Planarity : 0.004 0.049 3058 Dihedral : 10.797 88.034 2860 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.56 % Allowed : 18.14 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.18), residues: 2132 helix: 0.49 (0.21), residues: 666 sheet: -0.94 (0.24), residues: 475 loop : -2.15 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.019 0.001 TYR C 898 PHE 0.011 0.001 PHE A 788 TRP 0.009 0.001 TRP B 29 HIS 0.008 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00264 (18096) covalent geometry : angle 0.53295 (24675) hydrogen bonds : bond 0.03657 ( 601) hydrogen bonds : angle 4.71586 ( 1666) metal coordination : bond 0.00524 ( 12) metal coordination : angle 3.99232 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.7900 (tpp) cc_final: 0.7637 (mmt) REVERT: C 784 MET cc_start: 0.7699 (tmm) cc_final: 0.7383 (tmm) REVERT: C 1060 PHE cc_start: 0.8044 (m-80) cc_final: 0.7709 (m-80) REVERT: D 95 LYS cc_start: 0.7363 (tttt) cc_final: 0.7126 (tttt) REVERT: A 98 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7223 (ppp) REVERT: A 590 MET cc_start: 0.0680 (mmp) cc_final: 0.0316 (ptm) REVERT: A 715 MET cc_start: 0.6808 (mpp) cc_final: 0.6233 (mpp) REVERT: A 817 GLN cc_start: 0.7154 (mt0) cc_final: 0.6457 (tt0) REVERT: A 823 MET cc_start: 0.7344 (ppp) cc_final: 0.6703 (ppp) outliers start: 29 outliers final: 25 residues processed: 221 average time/residue: 0.1080 time to fit residues: 37.5531 Evaluate side-chains 218 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 967 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1143 VAL Chi-restraints excluded: chain C residue 1195 MET Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 130 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 57 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 30.0000 chunk 6 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 0.0370 chunk 99 optimal weight: 0.9980 chunk 170 optimal weight: 8.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.188568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143912 restraints weight = 23785.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140767 restraints weight = 21743.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142201 restraints weight = 20132.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142890 restraints weight = 13380.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143008 restraints weight = 12210.227| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18108 Z= 0.091 Angle : 0.515 10.967 24693 Z= 0.257 Chirality : 0.041 0.166 2833 Planarity : 0.004 0.046 3058 Dihedral : 10.696 90.935 2860 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.40 % Allowed : 18.46 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2132 helix: 0.66 (0.21), residues: 668 sheet: -0.70 (0.25), residues: 462 loop : -2.07 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 590 TYR 0.023 0.001 TYR C 898 PHE 0.009 0.001 PHE A 788 TRP 0.009 0.001 TRP B 29 HIS 0.007 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00201 (18096) covalent geometry : angle 0.50621 (24675) hydrogen bonds : bond 0.02922 ( 601) hydrogen bonds : angle 4.52710 ( 1666) metal coordination : bond 0.00438 ( 12) metal coordination : angle 3.61728 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 609 MET cc_start: 0.5308 (ptp) cc_final: 0.5049 (ptp) REVERT: C 675 MET cc_start: 0.7855 (tpp) cc_final: 0.7500 (mmm) REVERT: C 1060 PHE cc_start: 0.8003 (m-80) cc_final: 0.7667 (m-80) REVERT: D 95 LYS cc_start: 0.7316 (tttt) cc_final: 0.7057 (tttt) REVERT: A 83 ASP cc_start: 0.8424 (t0) cc_final: 0.8039 (t0) REVERT: A 98 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7197 (ppp) REVERT: A 715 MET cc_start: 0.7032 (mpp) cc_final: 0.6566 (mpp) REVERT: A 817 GLN cc_start: 0.7083 (mt0) cc_final: 0.6379 (tt0) REVERT: A 823 MET cc_start: 0.7360 (ppp) cc_final: 0.6900 (ppp) REVERT: A 1214 ARG cc_start: 0.7926 (tmm-80) cc_final: 0.7650 (ttt180) outliers start: 26 outliers final: 20 residues processed: 237 average time/residue: 0.1092 time to fit residues: 40.7808 Evaluate side-chains 222 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 967 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 40 optimal weight: 0.6980 chunk 139 optimal weight: 20.0000 chunk 76 optimal weight: 0.2980 chunk 185 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 193 optimal weight: 0.0010 chunk 22 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 670 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.188283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143538 restraints weight = 23713.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140049 restraints weight = 20953.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141805 restraints weight = 19700.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142254 restraints weight = 13682.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142394 restraints weight = 12692.579| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18108 Z= 0.094 Angle : 0.524 10.454 24693 Z= 0.260 Chirality : 0.041 0.165 2833 Planarity : 0.004 0.046 3058 Dihedral : 10.667 90.558 2860 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.24 % Allowed : 18.84 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.18), residues: 2132 helix: 0.58 (0.21), residues: 681 sheet: -0.66 (0.25), residues: 463 loop : -2.03 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.017 0.001 TYR C 898 PHE 0.009 0.001 PHE A 788 TRP 0.008 0.001 TRP B 29 HIS 0.007 0.000 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00211 (18096) covalent geometry : angle 0.51459 (24675) hydrogen bonds : bond 0.03059 ( 601) hydrogen bonds : angle 4.47117 ( 1666) metal coordination : bond 0.00322 ( 12) metal coordination : angle 3.63324 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.7853 (tpp) cc_final: 0.7648 (mmt) REVERT: C 1060 PHE cc_start: 0.8072 (m-80) cc_final: 0.7728 (m-80) REVERT: C 1246 MET cc_start: 0.8457 (mmm) cc_final: 0.8112 (mmm) REVERT: A 83 ASP cc_start: 0.8394 (t0) cc_final: 0.8011 (t0) REVERT: A 98 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7099 (ppp) REVERT: A 715 MET cc_start: 0.6901 (mpp) cc_final: 0.6470 (mpp) REVERT: A 817 GLN cc_start: 0.7085 (mt0) cc_final: 0.6393 (tt0) REVERT: A 823 MET cc_start: 0.7378 (ppp) cc_final: 0.6906 (ppp) REVERT: A 1214 ARG cc_start: 0.7883 (tmm-80) cc_final: 0.7630 (ttt180) REVERT: B 73 LEU cc_start: 0.8858 (tt) cc_final: 0.8641 (tt) outliers start: 23 outliers final: 19 residues processed: 220 average time/residue: 0.1159 time to fit residues: 40.3879 Evaluate side-chains 220 residues out of total 1858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 544 LEU Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 805 TYR Chi-restraints excluded: chain C residue 967 GLU Chi-restraints excluded: chain C residue 1031 VAL Chi-restraints excluded: chain C residue 1066 LEU Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1205 GLU Chi-restraints excluded: chain D residue 14 GLN Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain B residue 27 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 145 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.0670 chunk 164 optimal weight: 40.0000 chunk 203 optimal weight: 0.0980 chunk 185 optimal weight: 0.5980 chunk 204 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 HIS A 104 GLN ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.184380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139797 restraints weight = 23950.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.136158 restraints weight = 21540.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138643 restraints weight = 20930.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138440 restraints weight = 12975.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139825 restraints weight = 11804.314| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18108 Z= 0.134 Angle : 0.573 10.802 24693 Z= 0.284 Chirality : 0.043 0.165 2833 Planarity : 0.004 0.049 3058 Dihedral : 10.705 87.676 2860 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.18 % Allowed : 19.11 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.18), residues: 2132 helix: 0.52 (0.21), residues: 676 sheet: -0.76 (0.25), residues: 463 loop : -2.07 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.014 0.001 TYR C 898 PHE 0.012 0.001 PHE A 955 TRP 0.009 0.001 TRP C1216 HIS 0.006 0.001 HIS C 550 Details of bonding type rmsd covalent geometry : bond 0.00318 (18096) covalent geometry : angle 0.55891 (24675) hydrogen bonds : bond 0.03922 ( 601) hydrogen bonds : angle 4.62280 ( 1666) metal coordination : bond 0.00575 ( 12) metal coordination : angle 4.66094 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.43 seconds wall clock time: 41 minutes 26.31 seconds (2486.31 seconds total)