Starting phenix.real_space_refine on Thu Dec 26 02:26:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6q_27922/12_2024/8e6q_27922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6q_27922/12_2024/8e6q_27922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e6q_27922/12_2024/8e6q_27922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6q_27922/12_2024/8e6q_27922.map" model { file = "/net/cci-nas-00/data/ceres_data/8e6q_27922/12_2024/8e6q_27922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6q_27922/12_2024/8e6q_27922.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 sd= 0.059 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 168 5.16 5 C 26360 2.51 5 N 7144 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 40888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 10150 Classifications: {'peptide': 1348} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'CIS': 1, 'PTRANS': 66, 'TRANS': 1280} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 35, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 469 Chain: "B" Number of atoms: 10150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 10150 Classifications: {'peptide': 1348} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'CIS': 1, 'PTRANS': 66, 'TRANS': 1280} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 35, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 469 Chain: "C" Number of atoms: 10150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 10150 Classifications: {'peptide': 1348} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'CIS': 1, 'PTRANS': 66, 'TRANS': 1280} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 35, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 469 Chain: "D" Number of atoms: 10150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 10150 Classifications: {'peptide': 1348} Incomplete info: {'truncation_to_alanine': 206} Link IDs: {'CIS': 1, 'PTRANS': 66, 'TRANS': 1280} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 740 Unresolved non-hydrogen angles: 926 Unresolved non-hydrogen dihedrals: 603 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 35, 'ASP:plan': 20} Unresolved non-hydrogen planarities: 469 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.81, per 1000 atoms: 0.56 Number of scatterers: 40888 At special positions: 0 Unit cell: (171.72, 172.78, 166.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 16 15.00 O 7200 8.00 N 7144 7.00 C 26360 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: 10.75 Conformation dependent library (CDL) restraints added in 5.6 seconds 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10168 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 28 sheets defined 53.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.708A pdb=" N SER A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.667A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.506A pdb=" N ILE A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.912A pdb=" N PHE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 312 Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.587A pdb=" N THR A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.526A pdb=" N ASP A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.599A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.652A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 395 through 412 removed outlier: 4.277A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 444 removed outlier: 3.946A pdb=" N ALA A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.902A pdb=" N LEU A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.581A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.608A pdb=" N ALA A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 removed outlier: 4.051A pdb=" N LYS A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.869A pdb=" N LEU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.610A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 4.022A pdb=" N ASP A 584 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.702A pdb=" N LEU A 625 " --> pdb=" O PRO A 621 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.598A pdb=" N GLY A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 671 through 696 removed outlier: 4.052A pdb=" N LYS A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 709 through 713 removed outlier: 4.037A pdb=" N GLY A 713 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 723 removed outlier: 3.607A pdb=" N LEU A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.563A pdb=" N VAL A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 731' Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 752 through 762 removed outlier: 3.562A pdb=" N VAL A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU A 758 " --> pdb=" O TRP A 754 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS A 759 " --> pdb=" O ARG A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 767 Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.935A pdb=" N ALA A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 819 removed outlier: 3.665A pdb=" N LEU A 810 " --> pdb=" O TYR A 806 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 811 " --> pdb=" O PHE A 807 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 817 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 848 removed outlier: 3.614A pdb=" N TYR A 833 " --> pdb=" O GLU A 829 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 865 removed outlier: 3.836A pdb=" N ALA A 860 " --> pdb=" O LEU A 856 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 861 " --> pdb=" O MET A 857 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 863 " --> pdb=" O LYS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 888 removed outlier: 4.055A pdb=" N CYS A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 removed outlier: 3.855A pdb=" N LEU A 899 " --> pdb=" O GLY A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 913 removed outlier: 3.510A pdb=" N CYS A 907 " --> pdb=" O PHE A 903 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 956 removed outlier: 3.938A pdb=" N ILE A 926 " --> pdb=" O PRO A 922 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 927 " --> pdb=" O LYS A 923 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 935 " --> pdb=" O MET A 931 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 948 " --> pdb=" O TRP A 944 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN A 953 " --> pdb=" O GLY A 949 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 977 removed outlier: 5.361A pdb=" N HIS A 973 " --> pdb=" O GLY A 969 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 975 " --> pdb=" O VAL A 971 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 976 " --> pdb=" O TYR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 1021 through 1037 removed outlier: 3.573A pdb=" N LEU A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1055 removed outlier: 3.889A pdb=" N ILE A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A1046 " --> pdb=" O ASN A1042 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR A1051 " --> pdb=" O MET A1047 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1055 " --> pdb=" O THR A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1076 removed outlier: 4.329A pdb=" N HIS A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP A1069 " --> pdb=" O PHE A1065 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A1070 " --> pdb=" O GLN A1066 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 removed outlier: 3.798A pdb=" N SER A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A1092 " --> pdb=" O SER A1088 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A1093 " --> pdb=" O HIS A1089 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1143 removed outlier: 3.633A pdb=" N ALA A1120 " --> pdb=" O ASN A1116 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TRP A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A1141 " --> pdb=" O GLN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1160 removed outlier: 3.594A pdb=" N GLU A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 4.033A pdb=" N ASP A1291 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1404 Processing helix chain 'A' and resid 1410 through 1418 removed outlier: 3.762A pdb=" N PHE A1414 " --> pdb=" O HIS A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1463 removed outlier: 3.766A pdb=" N ARG A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.555A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1499 No H-bonds generated for 'chain 'A' and resid 1497 through 1499' Processing helix chain 'B' and resid 57 through 67 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.667A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.505A pdb=" N ILE B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.911A pdb=" N PHE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.588A pdb=" N THR B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.525A pdb=" N ASP B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.599A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 removed outlier: 3.651A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 395 through 412 removed outlier: 4.276A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 444 removed outlier: 3.946A pdb=" N ALA B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU B 437 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.901A pdb=" N LEU B 456 " --> pdb=" O TRP B 452 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.580A pdb=" N ALA B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.607A pdb=" N ALA B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 removed outlier: 4.051A pdb=" N LYS B 501 " --> pdb=" O PRO B 497 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 524 Processing helix chain 'B' and resid 530 through 543 removed outlier: 3.870A pdb=" N LEU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.611A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 4.022A pdb=" N ASP B 584 " --> pdb=" O ARG B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.702A pdb=" N LEU B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.598A pdb=" N GLY B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 Processing helix chain 'B' and resid 671 through 696 removed outlier: 4.052A pdb=" N LYS B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 Processing helix chain 'B' and resid 709 through 713 removed outlier: 4.037A pdb=" N GLY B 713 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 723 removed outlier: 3.606A pdb=" N LEU B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU B 723 " --> pdb=" O GLN B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 731 removed outlier: 3.563A pdb=" N VAL B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 731 " --> pdb=" O MET B 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 726 through 731' Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 752 through 762 removed outlier: 3.562A pdb=" N VAL B 756 " --> pdb=" O GLY B 752 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 758 " --> pdb=" O TRP B 754 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS B 759 " --> pdb=" O ARG B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.934A pdb=" N ALA B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 819 removed outlier: 3.666A pdb=" N LEU B 810 " --> pdb=" O TYR B 806 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS B 811 " --> pdb=" O PHE B 807 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 817 " --> pdb=" O PHE B 813 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 848 removed outlier: 3.614A pdb=" N TYR B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU B 843 " --> pdb=" O LEU B 839 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B 844 " --> pdb=" O VAL B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 865 removed outlier: 3.836A pdb=" N ALA B 860 " --> pdb=" O LEU B 856 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 861 " --> pdb=" O MET B 857 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU B 862 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 863 " --> pdb=" O LYS B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 888 removed outlier: 4.055A pdb=" N CYS B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 899 removed outlier: 3.855A pdb=" N LEU B 899 " --> pdb=" O GLY B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 913 removed outlier: 3.511A pdb=" N CYS B 907 " --> pdb=" O PHE B 903 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 956 removed outlier: 3.938A pdb=" N ILE B 926 " --> pdb=" O PRO B 922 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 927 " --> pdb=" O LYS B 923 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 935 " --> pdb=" O MET B 931 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 948 " --> pdb=" O TRP B 944 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 953 " --> pdb=" O GLY B 949 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 954 " --> pdb=" O VAL B 950 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE B 955 " --> pdb=" O ALA B 951 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 977 removed outlier: 5.361A pdb=" N HIS B 973 " --> pdb=" O GLY B 969 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER B 974 " --> pdb=" O ALA B 970 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR B 975 " --> pdb=" O VAL B 971 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 976 " --> pdb=" O TYR B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 988 Processing helix chain 'B' and resid 1021 through 1037 removed outlier: 3.572A pdb=" N LEU B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1055 removed outlier: 3.889A pdb=" N ILE B1045 " --> pdb=" O LEU B1041 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B1046 " --> pdb=" O ASN B1042 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B1051 " --> pdb=" O MET B1047 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1076 removed outlier: 4.329A pdb=" N HIS B1068 " --> pdb=" O LYS B1064 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP B1069 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B1076 " --> pdb=" O GLU B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1099 removed outlier: 3.799A pdb=" N SER B1088 " --> pdb=" O PHE B1084 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B1090 " --> pdb=" O LEU B1086 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B1092 " --> pdb=" O SER B1088 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B1093 " --> pdb=" O HIS B1089 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B1096 " --> pdb=" O LEU B1092 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B1098 " --> pdb=" O ILE B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1143 removed outlier: 3.634A pdb=" N ALA B1120 " --> pdb=" O ASN B1116 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP B1124 " --> pdb=" O ALA B1120 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B1141 " --> pdb=" O GLN B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1160 removed outlier: 3.595A pdb=" N GLU B1149 " --> pdb=" O GLU B1145 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B1159 " --> pdb=" O VAL B1155 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP B1160 " --> pdb=" O ASP B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1292 removed outlier: 4.032A pdb=" N ASP B1291 " --> pdb=" O PRO B1288 " (cutoff:3.500A) Processing helix chain 'B' and resid 1397 through 1404 Processing helix chain 'B' and resid 1410 through 1418 removed outlier: 3.763A pdb=" N PHE B1414 " --> pdb=" O HIS B1410 " (cutoff:3.500A) Processing helix chain 'B' and resid 1455 through 1463 removed outlier: 3.766A pdb=" N ARG B1459 " --> pdb=" O VAL B1455 " (cutoff:3.500A) Processing helix chain 'B' and resid 1485 through 1496 removed outlier: 3.555A pdb=" N LEU B1491 " --> pdb=" O ASN B1487 " (cutoff:3.500A) Processing helix chain 'B' and resid 1497 through 1499 No H-bonds generated for 'chain 'B' and resid 1497 through 1499' Processing helix chain 'C' and resid 57 through 67 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 114 through 119 Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.666A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 202 removed outlier: 3.505A pdb=" N ILE C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.911A pdb=" N PHE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.589A pdb=" N THR C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.526A pdb=" N ASP C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.599A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 387 removed outlier: 3.651A pdb=" N VAL C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 395 through 412 removed outlier: 4.278A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 444 removed outlier: 3.946A pdb=" N ALA C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.902A pdb=" N LEU C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN C 463 " --> pdb=" O ALA C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.581A pdb=" N ALA C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 484 through 495 removed outlier: 3.608A pdb=" N ALA C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 506 removed outlier: 4.052A pdb=" N LYS C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 515 through 524 Processing helix chain 'C' and resid 530 through 543 removed outlier: 3.869A pdb=" N LEU C 540 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.611A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 removed outlier: 4.022A pdb=" N ASP C 584 " --> pdb=" O ARG C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.701A pdb=" N LEU C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 644 removed outlier: 3.598A pdb=" N GLY C 639 " --> pdb=" O ARG C 635 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 644 " --> pdb=" O ILE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 664 Processing helix chain 'C' and resid 671 through 696 removed outlier: 4.052A pdb=" N LYS C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 Processing helix chain 'C' and resid 709 through 713 removed outlier: 4.037A pdb=" N GLY C 713 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 723 removed outlier: 3.606A pdb=" N LEU C 722 " --> pdb=" O LEU C 718 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 731 removed outlier: 3.564A pdb=" N VAL C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 731 " --> pdb=" O MET C 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 726 through 731' Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.562A pdb=" N VAL C 756 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU C 758 " --> pdb=" O TRP C 754 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS C 759 " --> pdb=" O ARG C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 767 Processing helix chain 'C' and resid 783 through 794 removed outlier: 3.934A pdb=" N ALA C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 819 removed outlier: 3.666A pdb=" N LEU C 810 " --> pdb=" O TYR C 806 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS C 811 " --> pdb=" O PHE C 807 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 817 " --> pdb=" O PHE C 813 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 848 removed outlier: 3.614A pdb=" N TYR C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 842 " --> pdb=" O SER C 838 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU C 843 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET C 844 " --> pdb=" O VAL C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 865 removed outlier: 3.837A pdb=" N ALA C 860 " --> pdb=" O LEU C 856 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 861 " --> pdb=" O MET C 857 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU C 862 " --> pdb=" O LYS C 858 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR C 863 " --> pdb=" O LYS C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 888 removed outlier: 4.056A pdb=" N CYS C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 899 removed outlier: 3.855A pdb=" N LEU C 899 " --> pdb=" O GLY C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 913 removed outlier: 3.510A pdb=" N CYS C 907 " --> pdb=" O PHE C 903 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 956 removed outlier: 3.937A pdb=" N ILE C 926 " --> pdb=" O PRO C 922 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 927 " --> pdb=" O LYS C 923 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 935 " --> pdb=" O MET C 931 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 948 " --> pdb=" O TRP C 944 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C 951 " --> pdb=" O SER C 947 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C 953 " --> pdb=" O GLY C 949 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 954 " --> pdb=" O VAL C 950 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 955 " --> pdb=" O ALA C 951 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU C 956 " --> pdb=" O LYS C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 977 removed outlier: 5.361A pdb=" N HIS C 973 " --> pdb=" O GLY C 969 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER C 974 " --> pdb=" O ALA C 970 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C 975 " --> pdb=" O VAL C 971 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 976 " --> pdb=" O TYR C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 988 Processing helix chain 'C' and resid 1021 through 1037 removed outlier: 3.573A pdb=" N LEU C1033 " --> pdb=" O LEU C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1055 removed outlier: 3.889A pdb=" N ILE C1045 " --> pdb=" O LEU C1041 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C1046 " --> pdb=" O ASN C1042 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR C1051 " --> pdb=" O MET C1047 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C1055 " --> pdb=" O THR C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1076 removed outlier: 4.330A pdb=" N HIS C1068 " --> pdb=" O LYS C1064 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP C1069 " --> pdb=" O PHE C1065 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C1076 " --> pdb=" O GLU C1072 " (cutoff:3.500A) Processing helix chain 'C' and resid 1084 through 1099 removed outlier: 3.798A pdb=" N SER C1088 " --> pdb=" O PHE C1084 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C1090 " --> pdb=" O LEU C1086 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C1092 " --> pdb=" O SER C1088 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE C1093 " --> pdb=" O HIS C1089 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C1096 " --> pdb=" O LEU C1092 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C1098 " --> pdb=" O ILE C1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1143 removed outlier: 3.633A pdb=" N ALA C1120 " --> pdb=" O ASN C1116 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TRP C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C1141 " --> pdb=" O GLN C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1160 removed outlier: 3.595A pdb=" N GLU C1149 " --> pdb=" O GLU C1145 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C1159 " --> pdb=" O VAL C1155 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP C1160 " --> pdb=" O ASP C1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 1288 through 1292 removed outlier: 4.033A pdb=" N ASP C1291 " --> pdb=" O PRO C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1397 through 1404 Processing helix chain 'C' and resid 1410 through 1418 removed outlier: 3.763A pdb=" N PHE C1414 " --> pdb=" O HIS C1410 " (cutoff:3.500A) Processing helix chain 'C' and resid 1455 through 1463 removed outlier: 3.766A pdb=" N ARG C1459 " --> pdb=" O VAL C1455 " (cutoff:3.500A) Processing helix chain 'C' and resid 1485 through 1496 removed outlier: 3.555A pdb=" N LEU C1491 " --> pdb=" O ASN C1487 " (cutoff:3.500A) Processing helix chain 'C' and resid 1497 through 1499 No H-bonds generated for 'chain 'C' and resid 1497 through 1499' Processing helix chain 'D' and resid 57 through 67 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.668A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.504A pdb=" N ILE D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 194 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.911A pdb=" N PHE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 312 Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.589A pdb=" N THR D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.525A pdb=" N ASP D 361 " --> pdb=" O GLY D 357 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.599A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 387 removed outlier: 3.651A pdb=" N VAL D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 412 removed outlier: 4.276A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 444 removed outlier: 3.946A pdb=" N ALA D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU D 437 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 444 " --> pdb=" O ALA D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.902A pdb=" N LEU D 456 " --> pdb=" O TRP D 452 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN D 463 " --> pdb=" O ALA D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.580A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 484 through 495 removed outlier: 3.608A pdb=" N ALA D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 506 removed outlier: 4.052A pdb=" N LYS D 501 " --> pdb=" O PRO D 497 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 502 " --> pdb=" O GLU D 498 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 515 through 524 Processing helix chain 'D' and resid 530 through 543 removed outlier: 3.869A pdb=" N LEU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.610A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 584 removed outlier: 4.022A pdb=" N ASP D 584 " --> pdb=" O ARG D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 632 removed outlier: 3.702A pdb=" N LEU D 625 " --> pdb=" O PRO D 621 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.598A pdb=" N GLY D 639 " --> pdb=" O ARG D 635 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN D 644 " --> pdb=" O ILE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 664 Processing helix chain 'D' and resid 671 through 696 removed outlier: 4.052A pdb=" N LYS D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 Processing helix chain 'D' and resid 709 through 713 removed outlier: 4.038A pdb=" N GLY D 713 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 723 removed outlier: 3.606A pdb=" N LEU D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU D 723 " --> pdb=" O GLN D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 731 removed outlier: 3.563A pdb=" N VAL D 730 " --> pdb=" O ASP D 726 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER D 731 " --> pdb=" O MET D 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 726 through 731' Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 752 through 762 removed outlier: 3.563A pdb=" N VAL D 756 " --> pdb=" O GLY D 752 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 757 " --> pdb=" O LEU D 753 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU D 758 " --> pdb=" O TRP D 754 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS D 759 " --> pdb=" O ARG D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 767 Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.934A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 819 removed outlier: 3.666A pdb=" N LEU D 810 " --> pdb=" O TYR D 806 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D 811 " --> pdb=" O PHE D 807 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 817 " --> pdb=" O PHE D 813 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 848 removed outlier: 3.614A pdb=" N TYR D 833 " --> pdb=" O GLU D 829 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU D 843 " --> pdb=" O LEU D 839 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET D 844 " --> pdb=" O VAL D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 865 removed outlier: 3.836A pdb=" N ALA D 860 " --> pdb=" O LEU D 856 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 861 " --> pdb=" O MET D 857 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU D 862 " --> pdb=" O LYS D 858 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR D 863 " --> pdb=" O LYS D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 888 removed outlier: 4.055A pdb=" N CYS D 885 " --> pdb=" O ALA D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 899 removed outlier: 3.855A pdb=" N LEU D 899 " --> pdb=" O GLY D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 913 removed outlier: 3.511A pdb=" N CYS D 907 " --> pdb=" O PHE D 903 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 909 " --> pdb=" O LEU D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 956 removed outlier: 3.937A pdb=" N ILE D 926 " --> pdb=" O PRO D 922 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 927 " --> pdb=" O LYS D 923 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 935 " --> pdb=" O MET D 931 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 948 " --> pdb=" O TRP D 944 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA D 951 " --> pdb=" O SER D 947 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN D 953 " --> pdb=" O GLY D 949 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 954 " --> pdb=" O VAL D 950 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE D 955 " --> pdb=" O ALA D 951 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU D 956 " --> pdb=" O LYS D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 977 removed outlier: 5.360A pdb=" N HIS D 973 " --> pdb=" O GLY D 969 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER D 974 " --> pdb=" O ALA D 970 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR D 975 " --> pdb=" O VAL D 971 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 976 " --> pdb=" O TYR D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 988 Processing helix chain 'D' and resid 1021 through 1037 removed outlier: 3.573A pdb=" N LEU D1033 " --> pdb=" O LEU D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1055 removed outlier: 3.889A pdb=" N ILE D1045 " --> pdb=" O LEU D1041 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D1046 " --> pdb=" O ASN D1042 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR D1051 " --> pdb=" O MET D1047 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D1055 " --> pdb=" O THR D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1076 removed outlier: 4.330A pdb=" N HIS D1068 " --> pdb=" O LYS D1064 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP D1069 " --> pdb=" O PHE D1065 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D1070 " --> pdb=" O GLN D1066 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D1076 " --> pdb=" O GLU D1072 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1099 removed outlier: 3.799A pdb=" N SER D1088 " --> pdb=" O PHE D1084 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D1092 " --> pdb=" O SER D1088 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE D1093 " --> pdb=" O HIS D1089 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D1096 " --> pdb=" O LEU D1092 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D1098 " --> pdb=" O ILE D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1143 removed outlier: 3.633A pdb=" N ALA D1120 " --> pdb=" O ASN D1116 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TRP D1124 " --> pdb=" O ALA D1120 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D1141 " --> pdb=" O GLN D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1160 removed outlier: 3.594A pdb=" N GLU D1149 " --> pdb=" O GLU D1145 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D1158 " --> pdb=" O LYS D1154 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D1159 " --> pdb=" O VAL D1155 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP D1160 " --> pdb=" O ASP D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1288 through 1292 removed outlier: 4.033A pdb=" N ASP D1291 " --> pdb=" O PRO D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1397 through 1404 Processing helix chain 'D' and resid 1410 through 1418 removed outlier: 3.763A pdb=" N PHE D1414 " --> pdb=" O HIS D1410 " (cutoff:3.500A) Processing helix chain 'D' and resid 1455 through 1463 removed outlier: 3.767A pdb=" N ARG D1459 " --> pdb=" O VAL D1455 " (cutoff:3.500A) Processing helix chain 'D' and resid 1485 through 1496 removed outlier: 3.555A pdb=" N LEU D1491 " --> pdb=" O ASN D1487 " (cutoff:3.500A) Processing helix chain 'D' and resid 1497 through 1499 No H-bonds generated for 'chain 'D' and resid 1497 through 1499' Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 7.000A pdb=" N TYR A 264 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL A 131 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 128 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 205 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL A 241 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR A 207 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR A 243 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 171 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLY A 208 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N VAL A 173 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 170 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 328 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A 172 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 351 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS A 327 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1275 through 1277 removed outlier: 3.793A pdb=" N ARG A1336 " --> pdb=" O TYR A1276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1303 through 1305 Processing sheet with id=AA5, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AA6, first strand: chain 'A' and resid 1390 through 1391 removed outlier: 5.883A pdb=" N GLY A1343 " --> pdb=" O TRP A1439 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A1441 " --> pdb=" O GLY A1343 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN A1345 " --> pdb=" O GLU A1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A1443 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A1347 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL A1445 " --> pdb=" O THR A1347 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE A1440 " --> pdb=" O TYR A1428 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR A1428 " --> pdb=" O ILE A1440 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A1442 " --> pdb=" O LYS A1426 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS A1426 " --> pdb=" O THR A1442 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA A1444 " --> pdb=" O VAL A1424 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1390 through 1391 removed outlier: 5.883A pdb=" N GLY A1343 " --> pdb=" O TRP A1439 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A1441 " --> pdb=" O GLY A1343 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN A1345 " --> pdb=" O GLU A1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A1443 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A1347 " --> pdb=" O VAL A1443 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL A1445 " --> pdb=" O THR A1347 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET A1351 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE A1449 " --> pdb=" O MET A1351 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A1353 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A1474 " --> pdb=" O VAL A1376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 264 removed outlier: 7.001A pdb=" N TYR B 264 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL B 131 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 128 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 205 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 241 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR B 207 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N THR B 243 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 171 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLY B 208 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N VAL B 173 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 170 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL B 328 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 172 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL B 351 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 327 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1275 through 1277 removed outlier: 3.792A pdb=" N ARG B1336 " --> pdb=" O TYR B1276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1303 through 1305 Processing sheet with id=AB3, first strand: chain 'B' and resid 1319 through 1320 Processing sheet with id=AB4, first strand: chain 'B' and resid 1390 through 1391 removed outlier: 5.883A pdb=" N GLY B1343 " --> pdb=" O TRP B1439 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU B1441 " --> pdb=" O GLY B1343 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN B1345 " --> pdb=" O GLU B1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B1443 " --> pdb=" O ASN B1345 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR B1347 " --> pdb=" O VAL B1443 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL B1445 " --> pdb=" O THR B1347 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE B1440 " --> pdb=" O TYR B1428 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR B1428 " --> pdb=" O ILE B1440 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B1442 " --> pdb=" O LYS B1426 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS B1426 " --> pdb=" O THR B1442 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA B1444 " --> pdb=" O VAL B1424 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1390 through 1391 removed outlier: 5.883A pdb=" N GLY B1343 " --> pdb=" O TRP B1439 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU B1441 " --> pdb=" O GLY B1343 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN B1345 " --> pdb=" O GLU B1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B1443 " --> pdb=" O ASN B1345 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR B1347 " --> pdb=" O VAL B1443 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL B1445 " --> pdb=" O THR B1347 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET B1351 " --> pdb=" O VAL B1447 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE B1449 " --> pdb=" O MET B1351 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR B1353 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B1474 " --> pdb=" O VAL B1376 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AB7, first strand: chain 'C' and resid 263 through 264 removed outlier: 7.000A pdb=" N TYR C 264 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 131 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 128 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 205 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL C 241 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR C 207 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N THR C 243 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 171 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLY C 208 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N VAL C 173 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU C 170 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 328 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 172 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL C 351 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS C 327 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1275 through 1277 removed outlier: 3.793A pdb=" N ARG C1336 " --> pdb=" O TYR C1276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1303 through 1305 Processing sheet with id=AC1, first strand: chain 'C' and resid 1319 through 1320 Processing sheet with id=AC2, first strand: chain 'C' and resid 1390 through 1391 removed outlier: 5.883A pdb=" N GLY C1343 " --> pdb=" O TRP C1439 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU C1441 " --> pdb=" O GLY C1343 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASN C1345 " --> pdb=" O GLU C1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C1443 " --> pdb=" O ASN C1345 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR C1347 " --> pdb=" O VAL C1443 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL C1445 " --> pdb=" O THR C1347 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE C1440 " --> pdb=" O TYR C1428 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR C1428 " --> pdb=" O ILE C1440 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1442 " --> pdb=" O LYS C1426 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS C1426 " --> pdb=" O THR C1442 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA C1444 " --> pdb=" O VAL C1424 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1390 through 1391 removed outlier: 5.883A pdb=" N GLY C1343 " --> pdb=" O TRP C1439 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU C1441 " --> pdb=" O GLY C1343 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASN C1345 " --> pdb=" O GLU C1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C1443 " --> pdb=" O ASN C1345 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR C1347 " --> pdb=" O VAL C1443 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL C1445 " --> pdb=" O THR C1347 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET C1351 " --> pdb=" O VAL C1447 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE C1449 " --> pdb=" O MET C1351 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR C1353 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C1474 " --> pdb=" O VAL C1376 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 68 through 71 Processing sheet with id=AC5, first strand: chain 'D' and resid 263 through 264 removed outlier: 7.000A pdb=" N TYR D 264 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL D 131 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 128 " --> pdb=" O TYR D 142 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE D 205 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL D 241 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR D 207 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N THR D 243 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE D 171 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLY D 208 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N VAL D 173 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU D 170 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL D 328 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER D 172 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL D 351 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS D 327 " --> pdb=" O VAL D 351 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1275 through 1277 removed outlier: 3.793A pdb=" N ARG D1336 " --> pdb=" O TYR D1276 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 1303 through 1305 Processing sheet with id=AC8, first strand: chain 'D' and resid 1319 through 1320 Processing sheet with id=AC9, first strand: chain 'D' and resid 1390 through 1391 removed outlier: 5.884A pdb=" N GLY D1343 " --> pdb=" O TRP D1439 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU D1441 " --> pdb=" O GLY D1343 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASN D1345 " --> pdb=" O GLU D1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D1443 " --> pdb=" O ASN D1345 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR D1347 " --> pdb=" O VAL D1443 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL D1445 " --> pdb=" O THR D1347 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE D1440 " --> pdb=" O TYR D1428 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR D1428 " --> pdb=" O ILE D1440 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D1442 " --> pdb=" O LYS D1426 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS D1426 " --> pdb=" O THR D1442 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA D1444 " --> pdb=" O VAL D1424 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 1390 through 1391 removed outlier: 5.884A pdb=" N GLY D1343 " --> pdb=" O TRP D1439 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU D1441 " --> pdb=" O GLY D1343 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASN D1345 " --> pdb=" O GLU D1441 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D1443 " --> pdb=" O ASN D1345 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR D1347 " --> pdb=" O VAL D1443 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL D1445 " --> pdb=" O THR D1347 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET D1351 " --> pdb=" O VAL D1447 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE D1449 " --> pdb=" O MET D1351 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR D1353 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D1474 " --> pdb=" O VAL D1376 " (cutoff:3.500A) 1718 hydrogen bonds defined for protein. 4926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.95 Time building geometry restraints manager: 12.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 11452 1.33 - 1.45: 7044 1.45 - 1.57: 23138 1.57 - 1.69: 34 1.69 - 1.81: 252 Bond restraints: 41920 Sorted by residual: bond pdb=" C5' APR D1602 " pdb=" O5' APR D1602 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.92e+00 bond pdb=" C5' APR A1602 " pdb=" O5' APR A1602 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.90e+00 bond pdb=" C5' APR C1602 " pdb=" O5' APR C1602 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 bond pdb=" C5' APR D1601 " pdb=" O5' APR D1601 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C5' APR B1602 " pdb=" O5' APR B1602 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.70e+00 ... (remaining 41915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 56854 4.07 - 8.13: 346 8.13 - 12.20: 28 12.20 - 16.26: 12 16.26 - 20.33: 4 Bond angle restraints: 57244 Sorted by residual: angle pdb=" CB LYS D1115 " pdb=" CG LYS D1115 " pdb=" CD LYS D1115 " ideal model delta sigma weight residual 111.30 127.17 -15.87 2.30e+00 1.89e-01 4.76e+01 angle pdb=" CB LYS A1115 " pdb=" CG LYS A1115 " pdb=" CD LYS A1115 " ideal model delta sigma weight residual 111.30 127.12 -15.82 2.30e+00 1.89e-01 4.73e+01 angle pdb=" CB LYS B1115 " pdb=" CG LYS B1115 " pdb=" CD LYS B1115 " ideal model delta sigma weight residual 111.30 127.12 -15.82 2.30e+00 1.89e-01 4.73e+01 angle pdb=" CB LYS C1115 " pdb=" CG LYS C1115 " pdb=" CD LYS C1115 " ideal model delta sigma weight residual 111.30 127.12 -15.82 2.30e+00 1.89e-01 4.73e+01 angle pdb=" CB MET B 930 " pdb=" CG MET B 930 " pdb=" SD MET B 930 " ideal model delta sigma weight residual 112.70 133.03 -20.33 3.00e+00 1.11e-01 4.59e+01 ... (remaining 57239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 22428 17.95 - 35.91: 1874 35.91 - 53.86: 382 53.86 - 71.82: 176 71.82 - 89.77: 108 Dihedral angle restraints: 24968 sinusoidal: 9276 harmonic: 15692 Sorted by residual: dihedral pdb=" CA GLY C 422 " pdb=" C GLY C 422 " pdb=" N LYS C 423 " pdb=" CA LYS C 423 " ideal model delta harmonic sigma weight residual -180.00 -122.03 -57.97 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLY D 422 " pdb=" C GLY D 422 " pdb=" N LYS D 423 " pdb=" CA LYS D 423 " ideal model delta harmonic sigma weight residual -180.00 -122.06 -57.94 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA GLY B 422 " pdb=" C GLY B 422 " pdb=" N LYS B 423 " pdb=" CA LYS B 423 " ideal model delta harmonic sigma weight residual -180.00 -122.09 -57.91 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 24965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5030 0.048 - 0.095: 1245 0.095 - 0.143: 256 0.143 - 0.191: 33 0.191 - 0.239: 16 Chirality restraints: 6580 Sorted by residual: chirality pdb=" C3' APR A1602 " pdb=" C2' APR A1602 " pdb=" C4' APR A1602 " pdb=" O3' APR A1602 " both_signs ideal model delta sigma weight residual False -2.54 -2.77 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' APR D1602 " pdb=" C2' APR D1602 " pdb=" C4' APR D1602 " pdb=" O3' APR D1602 " both_signs ideal model delta sigma weight residual False -2.54 -2.77 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' APR B1602 " pdb=" C2' APR B1602 " pdb=" C4' APR B1602 " pdb=" O3' APR B1602 " both_signs ideal model delta sigma weight residual False -2.54 -2.77 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 6577 not shown) Planarity restraints: 7264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 763 " 0.093 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO C 764 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO C 764 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO C 764 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 763 " -0.093 5.00e-02 4.00e+02 1.36e-01 2.95e+01 pdb=" N PRO A 764 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 763 " 0.093 5.00e-02 4.00e+02 1.36e-01 2.95e+01 pdb=" N PRO D 764 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO D 764 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO D 764 " 0.072 5.00e-02 4.00e+02 ... (remaining 7261 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 777 2.68 - 3.24: 40848 3.24 - 3.79: 63114 3.79 - 4.35: 82277 4.35 - 4.90: 129893 Nonbonded interactions: 316909 Sorted by model distance: nonbonded pdb=" NE2 GLN B1134 " pdb=" O SER C 230 " model vdw 2.130 3.120 nonbonded pdb=" NH1 ARG D1365 " pdb=" O LYS D1369 " model vdw 2.135 3.120 nonbonded pdb=" NH1 ARG A1365 " pdb=" O LYS A1369 " model vdw 2.135 3.120 nonbonded pdb=" NH1 ARG C1365 " pdb=" O LYS C1369 " model vdw 2.136 3.120 nonbonded pdb=" NE2 GLN C1134 " pdb=" O SER D 230 " model vdw 2.136 3.120 ... (remaining 316904 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 2.520 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: 0.070 Extract box with map and model: 1.680 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 92.150 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 : 0.004 0.083 41920 Z= 0.253 Angle : 0.861 20.330 57244 Z= 0.461 Chirality : 0.045 0.239 6580 Planarity : 0.007 0.136 7264 Dihedral : 16.423 89.771 14800 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.99 % Favored : 91.78 % Rotamer: Outliers : 1.76 % Allowed : 0.71 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.11), residues: 5368 helix: -0.50 (0.10), residues: 2436 sheet: -0.15 (0.30), residues: 320 loop : -2.80 (0.11), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 743 HIS 0.007 0.001 HIS D1502 PHE 0.013 0.001 PHE C 773 TYR 0.015 0.001 TYR C 155 ARG 0.013 0.001 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 667 time to evaluate : 4.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 TYR cc_start: 0.7590 (m-80) cc_final: 0.6017 (m-10) REVERT: A 653 LEU cc_start: 0.7235 (mt) cc_final: 0.6634 (mt) REVERT: A 669 THR cc_start: 0.7051 (t) cc_final: 0.6804 (t) REVERT: A 670 ASP cc_start: 0.8234 (p0) cc_final: 0.7945 (p0) REVERT: A 718 LEU cc_start: 0.8028 (tp) cc_final: 0.7759 (tp) REVERT: A 844 MET cc_start: 0.8346 (mtm) cc_final: 0.7171 (tmm) REVERT: A 877 LEU cc_start: 0.8243 (mt) cc_final: 0.7855 (pp) REVERT: A 911 MET cc_start: 0.8038 (mmp) cc_final: 0.7791 (mmm) REVERT: A 918 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7897 (mmtm) REVERT: B 122 MET cc_start: 0.8548 (mpp) cc_final: 0.8022 (mpp) REVERT: B 843 GLU cc_start: 0.8139 (mp0) cc_final: 0.7616 (mp0) REVERT: B 844 MET cc_start: 0.8683 (mtm) cc_final: 0.7562 (tmm) REVERT: B 847 LEU cc_start: 0.8539 (tt) cc_final: 0.8186 (tt) REVERT: B 930 MET cc_start: 0.2784 (OUTLIER) cc_final: 0.2358 (tpp) REVERT: B 1156 ASP cc_start: 0.8044 (m-30) cc_final: 0.7742 (m-30) REVERT: B 1351 MET cc_start: 0.1721 (ttm) cc_final: 0.1331 (ptp) REVERT: C 122 MET cc_start: 0.7594 (mpp) cc_final: 0.7111 (mpp) REVERT: C 207 THR cc_start: 0.7940 (t) cc_final: 0.7533 (t) REVERT: C 415 LEU cc_start: 0.4415 (mm) cc_final: 0.3434 (tt) REVERT: C 726 ASP cc_start: 0.6724 (m-30) cc_final: 0.6287 (m-30) REVERT: C 751 ASN cc_start: 0.5779 (p0) cc_final: 0.5480 (p0) REVERT: C 778 LEU cc_start: 0.7597 (mp) cc_final: 0.7307 (tp) REVERT: C 844 MET cc_start: 0.9185 (mtm) cc_final: 0.8255 (ptp) REVERT: C 868 TRP cc_start: 0.5753 (m100) cc_final: 0.4799 (m100) REVERT: C 911 MET cc_start: 0.7436 (mmp) cc_final: 0.7095 (mmm) REVERT: C 923 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8454 (ptmt) REVERT: C 1069 ASP cc_start: 0.8279 (t70) cc_final: 0.7955 (m-30) REVERT: D 336 THR cc_start: 0.6495 (m) cc_final: 0.6160 (p) REVERT: D 435 GLN cc_start: 0.8997 (pm20) cc_final: 0.8518 (pm20) REVERT: D 741 LYS cc_start: 0.7701 (tppp) cc_final: 0.7423 (tppp) REVERT: D 844 MET cc_start: 0.8922 (mtm) cc_final: 0.8093 (ptm) REVERT: D 911 MET cc_start: 0.7906 (mmp) cc_final: 0.7511 (mmp) REVERT: D 918 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7732 (mmtt) REVERT: D 923 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8376 (tttt) REVERT: D 931 MET cc_start: -0.2143 (tpp) cc_final: -0.2630 (tpp) outliers start: 69 outliers final: 21 residues processed: 697 average time/residue: 0.5226 time to fit residues: 600.9755 Evaluate side-chains 460 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 436 time to evaluate : 4.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 923 LYS Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1149 GLU Chi-restraints excluded: chain A residue 1365 ARG Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 731 SER Chi-restraints excluded: chain B residue 923 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 923 LYS Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain D residue 731 SER Chi-restraints excluded: chain D residue 923 LYS Chi-restraints excluded: chain D residue 925 ILE Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 1145 GLU Chi-restraints excluded: chain D residue 1365 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 2.9990 chunk 406 optimal weight: 0.0170 chunk 225 optimal weight: 9.9990 chunk 138 optimal weight: 30.0000 chunk 274 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 420 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 312 optimal weight: 2.9990 chunk 486 optimal weight: 20.0000 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 HIS ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 HIS ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1502 HIS ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 ASN C1137 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 732 HIS ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 41920 Z= 0.381 Angle : 0.825 11.024 57244 Z= 0.419 Chirality : 0.048 0.227 6580 Planarity : 0.006 0.093 7264 Dihedral : 10.228 94.451 6222 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.22 % Favored : 90.63 % Rotamer: Outliers : 2.47 % Allowed : 9.25 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.38 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.11), residues: 5368 helix: -0.49 (0.10), residues: 2428 sheet: -0.47 (0.27), residues: 380 loop : -2.73 (0.11), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 868 HIS 0.018 0.002 HIS A1089 PHE 0.024 0.002 PHE C 937 TYR 0.024 0.002 TYR D 833 ARG 0.024 0.001 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 459 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8229 (mpp) cc_final: 0.7881 (mpp) REVERT: A 215 MET cc_start: 0.5941 (ptp) cc_final: 0.5673 (ptp) REVERT: A 844 MET cc_start: 0.8414 (mtm) cc_final: 0.7442 (tmm) REVERT: A 868 TRP cc_start: 0.6081 (m100) cc_final: 0.4802 (m100) REVERT: A 912 HIS cc_start: 0.7860 (t70) cc_final: 0.7594 (t70) REVERT: A 918 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7834 (mmtt) REVERT: A 1137 GLN cc_start: 0.8261 (tp40) cc_final: 0.7907 (tm-30) REVERT: A 1141 LYS cc_start: 0.9269 (mtmt) cc_final: 0.8965 (mtmt) REVERT: A 1145 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: B 122 MET cc_start: 0.8533 (mpp) cc_final: 0.8068 (mpp) REVERT: B 168 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7381 (t0) REVERT: B 215 MET cc_start: 0.7746 (ptp) cc_final: 0.7473 (ptp) REVERT: B 295 TYR cc_start: 0.6027 (OUTLIER) cc_final: 0.5329 (m-10) REVERT: B 463 ASN cc_start: 0.8873 (t0) cc_final: 0.8487 (t0) REVERT: B 844 MET cc_start: 0.8720 (mtm) cc_final: 0.7678 (tmm) REVERT: B 868 TRP cc_start: 0.6026 (m100) cc_final: 0.5153 (m100) REVERT: B 912 HIS cc_start: 0.7281 (t70) cc_final: 0.6954 (t-170) REVERT: B 1149 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: B 1156 ASP cc_start: 0.8294 (m-30) cc_final: 0.8094 (m-30) REVERT: B 1484 LEU cc_start: 0.8220 (tp) cc_final: 0.7643 (tp) REVERT: C 122 MET cc_start: 0.8032 (mpp) cc_final: 0.7292 (mpp) REVERT: C 215 MET cc_start: 0.7438 (mpp) cc_final: 0.7021 (mtt) REVERT: C 505 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: C 692 GLU cc_start: 0.8561 (tp30) cc_final: 0.8143 (tp30) REVERT: C 835 TRP cc_start: 0.3770 (t-100) cc_final: 0.2958 (t-100) REVERT: C 843 GLU cc_start: 0.8171 (mp0) cc_final: 0.7841 (mp0) REVERT: C 844 MET cc_start: 0.9082 (mtm) cc_final: 0.8448 (ptp) REVERT: C 868 TRP cc_start: 0.5952 (m100) cc_final: 0.5249 (m100) REVERT: C 911 MET cc_start: 0.7566 (mmp) cc_final: 0.7329 (mmm) REVERT: C 923 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8581 (mmmt) REVERT: C 1385 TRP cc_start: 0.6644 (m100) cc_final: 0.5639 (m100) REVERT: D 760 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8080 (ptm) REVERT: D 844 MET cc_start: 0.8942 (mtm) cc_final: 0.8316 (ptp) REVERT: D 911 MET cc_start: 0.8179 (mmp) cc_final: 0.7739 (mmm) REVERT: D 918 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7811 (mmtt) REVERT: D 1072 GLU cc_start: 0.7853 (tt0) cc_final: 0.7619 (tm-30) outliers start: 97 outliers final: 53 residues processed: 523 average time/residue: 0.5563 time to fit residues: 486.0019 Evaluate side-chains 439 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 379 time to evaluate : 4.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 800 HIS Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1060 ASP Chi-restraints excluded: chain B residue 1090 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 800 HIS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 923 LYS Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 937 PHE Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1148 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 731 SER Chi-restraints excluded: chain D residue 760 MET Chi-restraints excluded: chain D residue 800 HIS Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 863 TYR Chi-restraints excluded: chain D residue 1138 PHE Chi-restraints excluded: chain D residue 1148 ILE Chi-restraints excluded: chain D residue 1151 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 50.0000 chunk 151 optimal weight: 20.0000 chunk 405 optimal weight: 50.0000 chunk 331 optimal weight: 0.6980 chunk 134 optimal weight: 30.0000 chunk 487 optimal weight: 1.9990 chunk 526 optimal weight: 5.9990 chunk 434 optimal weight: 7.9990 chunk 483 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 391 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 280 ASN A 346 ASN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 338 HIS ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1346 HIS C 280 ASN C 338 HIS ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 41920 Z= 0.326 Angle : 0.717 9.331 57244 Z= 0.367 Chirality : 0.045 0.214 6580 Planarity : 0.005 0.074 7264 Dihedral : 8.309 104.319 6171 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.63 % Favored : 91.23 % Rotamer: Outliers : 3.11 % Allowed : 12.41 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.38 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 5368 helix: -0.16 (0.10), residues: 2468 sheet: -0.50 (0.26), residues: 380 loop : -2.68 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 743 HIS 0.014 0.001 HIS A 559 PHE 0.034 0.002 PHE D 386 TYR 0.026 0.002 TYR B 833 ARG 0.006 0.001 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 408 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.6443 (ptp) cc_final: 0.6180 (ptp) REVERT: A 404 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6116 (mmtp) REVERT: A 488 MET cc_start: 0.8348 (tpt) cc_final: 0.7789 (tpt) REVERT: A 743 TRP cc_start: 0.7817 (OUTLIER) cc_final: 0.6723 (t60) REVERT: A 844 MET cc_start: 0.8530 (mtm) cc_final: 0.7398 (tmm) REVERT: A 918 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7854 (mmtt) REVERT: A 1047 MET cc_start: 0.5725 (ppp) cc_final: 0.5379 (ppp) REVERT: A 1145 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: A 1149 GLU cc_start: 0.8021 (mp0) cc_final: 0.7549 (mp0) REVERT: A 1371 MET cc_start: 0.6049 (mmm) cc_final: 0.5843 (mmm) REVERT: B 122 MET cc_start: 0.8603 (mpp) cc_final: 0.8112 (mpp) REVERT: B 215 MET cc_start: 0.7686 (ptp) cc_final: 0.7359 (ptp) REVERT: B 463 ASN cc_start: 0.8948 (t0) cc_final: 0.8587 (t0) REVERT: B 488 MET cc_start: 0.8348 (tpt) cc_final: 0.7971 (tpt) REVERT: B 844 MET cc_start: 0.8770 (mtm) cc_final: 0.7795 (tmm) REVERT: B 857 MET cc_start: 0.5508 (tpt) cc_final: 0.5215 (tpt) REVERT: B 911 MET cc_start: 0.7906 (mmm) cc_final: 0.7644 (mmm) REVERT: B 930 MET cc_start: 0.3458 (tpt) cc_final: 0.3054 (tpp) REVERT: B 1145 GLU cc_start: 0.8421 (mp0) cc_final: 0.7836 (mp0) REVERT: B 1149 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: B 1156 ASP cc_start: 0.8437 (m-30) cc_final: 0.8131 (m-30) REVERT: B 1491 LEU cc_start: 0.8295 (mp) cc_final: 0.7731 (tp) REVERT: C 122 MET cc_start: 0.8101 (mpp) cc_final: 0.7380 (mpp) REVERT: C 215 MET cc_start: 0.7589 (mpp) cc_final: 0.7271 (mtt) REVERT: C 692 GLU cc_start: 0.8555 (tp30) cc_final: 0.8262 (tp30) REVERT: C 743 TRP cc_start: 0.7891 (OUTLIER) cc_final: 0.7071 (t60) REVERT: C 744 TRP cc_start: 0.8334 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: C 844 MET cc_start: 0.9148 (mtm) cc_final: 0.8495 (ptp) REVERT: C 911 MET cc_start: 0.7754 (mmp) cc_final: 0.7372 (mmm) REVERT: C 923 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8708 (mmmt) REVERT: C 926 ILE cc_start: 0.8710 (mm) cc_final: 0.8495 (mm) REVERT: C 1149 GLU cc_start: 0.8019 (mp0) cc_final: 0.7452 (mp0) REVERT: C 1158 MET cc_start: 0.9023 (mmp) cc_final: 0.8710 (mmp) REVERT: C 1325 LEU cc_start: 0.7686 (mm) cc_final: 0.7413 (mm) REVERT: C 1385 TRP cc_start: 0.6738 (m100) cc_final: 0.5638 (m100) REVERT: D 196 LYS cc_start: 0.8883 (tttm) cc_final: 0.8602 (tttm) REVERT: D 215 MET cc_start: 0.6844 (ptp) cc_final: 0.6439 (ptp) REVERT: D 434 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7574 (mm) REVERT: D 501 LYS cc_start: 0.8515 (mtpt) cc_final: 0.7941 (mtmt) REVERT: D 537 GLN cc_start: 0.9167 (tp40) cc_final: 0.8863 (mm-40) REVERT: D 726 ASP cc_start: 0.7590 (m-30) cc_final: 0.7064 (m-30) REVERT: D 743 TRP cc_start: 0.7540 (OUTLIER) cc_final: 0.6592 (t60) REVERT: D 844 MET cc_start: 0.8990 (mtm) cc_final: 0.8333 (ptp) REVERT: D 868 TRP cc_start: 0.6129 (m100) cc_final: 0.5819 (m100) REVERT: D 918 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7896 (mmtt) REVERT: D 923 LYS cc_start: 0.9036 (tppt) cc_final: 0.8665 (ptmt) REVERT: D 1149 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7789 (mp0) REVERT: D 1158 MET cc_start: 0.9055 (mmm) cc_final: 0.8652 (mmt) outliers start: 122 outliers final: 59 residues processed: 507 average time/residue: 0.5149 time to fit residues: 436.5611 Evaluate side-chains 430 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 363 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 534 SER Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 743 TRP Chi-restraints excluded: chain C residue 744 TRP Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 730 VAL Chi-restraints excluded: chain D residue 731 SER Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 835 TRP Chi-restraints excluded: chain D residue 863 TYR Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 1138 PHE Chi-restraints excluded: chain D residue 1148 ILE Chi-restraints excluded: chain D residue 1151 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 20.0000 chunk 366 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 489 optimal weight: 6.9990 chunk 518 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 463 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 380 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 380 GLN B 444 GLN ** B 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1346 HIS C 380 GLN C 444 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN D 751 ASN ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41920 Z= 0.216 Angle : 0.656 13.720 57244 Z= 0.332 Chirality : 0.043 0.202 6580 Planarity : 0.005 0.063 7264 Dihedral : 7.472 102.360 6167 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.55 % Favored : 91.30 % Rotamer: Outliers : 2.91 % Allowed : 14.53 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.38 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 5368 helix: 0.13 (0.11), residues: 2480 sheet: -0.35 (0.26), residues: 372 loop : -2.58 (0.11), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1385 HIS 0.015 0.001 HIS C 559 PHE 0.026 0.001 PHE D 386 TYR 0.026 0.001 TYR B 833 ARG 0.010 0.000 ARG C 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 396 time to evaluate : 4.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.6536 (ptp) cc_final: 0.6178 (ptp) REVERT: A 404 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6132 (mmtp) REVERT: A 463 ASN cc_start: 0.8823 (t0) cc_final: 0.8586 (t0) REVERT: A 743 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.6560 (t60) REVERT: A 844 MET cc_start: 0.8515 (mtm) cc_final: 0.7453 (tmm) REVERT: A 918 LYS cc_start: 0.8415 (mtmt) cc_final: 0.7850 (mmtt) REVERT: A 1149 GLU cc_start: 0.7941 (mp0) cc_final: 0.7676 (mp0) REVERT: A 1371 MET cc_start: 0.5455 (mmm) cc_final: 0.4973 (mmm) REVERT: B 122 MET cc_start: 0.8615 (mpp) cc_final: 0.8092 (mpp) REVERT: B 215 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7497 (ptp) REVERT: B 295 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.4959 (m-10) REVERT: B 426 GLN cc_start: 0.4484 (OUTLIER) cc_final: 0.2649 (pm20) REVERT: B 444 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7899 (pp30) REVERT: B 463 ASN cc_start: 0.8919 (t0) cc_final: 0.8441 (t0) REVERT: B 488 MET cc_start: 0.8379 (tpt) cc_final: 0.8103 (tpt) REVERT: B 744 TRP cc_start: 0.8479 (OUTLIER) cc_final: 0.8199 (m-10) REVERT: B 844 MET cc_start: 0.8727 (mtm) cc_final: 0.7739 (tmm) REVERT: B 857 MET cc_start: 0.5675 (tpt) cc_final: 0.5384 (tpt) REVERT: B 930 MET cc_start: 0.3271 (tpt) cc_final: 0.2969 (tpt) REVERT: B 1145 GLU cc_start: 0.8336 (mp0) cc_final: 0.7745 (mp0) REVERT: B 1149 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: B 1156 ASP cc_start: 0.8377 (m-30) cc_final: 0.8123 (m-30) REVERT: B 1158 MET cc_start: 0.8646 (mmp) cc_final: 0.8349 (mmp) REVERT: C 122 MET cc_start: 0.8090 (mpp) cc_final: 0.7316 (mpp) REVERT: C 215 MET cc_start: 0.7697 (mpp) cc_final: 0.7335 (mtt) REVERT: C 435 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8989 (pm20) REVERT: C 505 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: C 558 MET cc_start: 0.8848 (mmm) cc_final: 0.8176 (mmt) REVERT: C 692 GLU cc_start: 0.8518 (tp30) cc_final: 0.8243 (tp30) REVERT: C 744 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.8038 (m-10) REVERT: C 778 LEU cc_start: 0.7437 (mt) cc_final: 0.6881 (tp) REVERT: C 844 MET cc_start: 0.9120 (mtm) cc_final: 0.8546 (ptp) REVERT: C 1149 GLU cc_start: 0.7878 (mp0) cc_final: 0.7607 (mp0) REVERT: C 1385 TRP cc_start: 0.6935 (m100) cc_final: 0.5834 (m100) REVERT: D 215 MET cc_start: 0.6772 (ptp) cc_final: 0.6467 (ptp) REVERT: D 434 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7461 (mm) REVERT: D 501 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8066 (mtpp) REVERT: D 537 GLN cc_start: 0.9162 (tp40) cc_final: 0.8836 (mm-40) REVERT: D 623 ARG cc_start: 0.7103 (mpt180) cc_final: 0.6887 (mpt180) REVERT: D 726 ASP cc_start: 0.7353 (m-30) cc_final: 0.6688 (m-30) REVERT: D 743 TRP cc_start: 0.7472 (OUTLIER) cc_final: 0.6522 (t60) REVERT: D 751 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8103 (p0) REVERT: D 760 MET cc_start: 0.8492 (ttt) cc_final: 0.8098 (ptm) REVERT: D 844 MET cc_start: 0.8962 (mtm) cc_final: 0.8354 (ptp) REVERT: D 911 MET cc_start: 0.8408 (mmm) cc_final: 0.8156 (mmm) REVERT: D 918 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7812 (mmtt) REVERT: D 923 LYS cc_start: 0.9100 (tppt) cc_final: 0.8674 (ptmt) REVERT: D 1158 MET cc_start: 0.8987 (mmm) cc_final: 0.8661 (mmt) REVERT: D 1347 THR cc_start: 0.7017 (OUTLIER) cc_final: 0.6789 (m) outliers start: 114 outliers final: 67 residues processed: 491 average time/residue: 0.5186 time to fit residues: 435.4935 Evaluate side-chains 445 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 363 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 744 TRP Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 744 TRP Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 934 VAL Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 751 ASN Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 1148 ILE Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1347 THR Chi-restraints excluded: chain D residue 1352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 4.9990 chunk 294 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 385 optimal weight: 20.0000 chunk 213 optimal weight: 10.0000 chunk 442 optimal weight: 5.9990 chunk 358 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 264 optimal weight: 20.0000 chunk 465 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1450 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41920 Z= 0.238 Angle : 0.661 16.744 57244 Z= 0.334 Chirality : 0.043 0.202 6580 Planarity : 0.005 0.060 7264 Dihedral : 7.068 62.276 6163 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.96 % Favored : 90.89 % Rotamer: Outliers : 3.13 % Allowed : 15.98 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5368 helix: 0.28 (0.11), residues: 2484 sheet: -0.27 (0.26), residues: 372 loop : -2.52 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 743 HIS 0.014 0.001 HIS C 559 PHE 0.022 0.001 PHE D 386 TYR 0.025 0.001 TYR A 833 ARG 0.009 0.000 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 383 time to evaluate : 4.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.6763 (ptp) cc_final: 0.6324 (ptp) REVERT: A 404 LYS cc_start: 0.6570 (OUTLIER) cc_final: 0.6210 (mmtp) REVERT: A 426 GLN cc_start: 0.3532 (OUTLIER) cc_final: 0.1523 (pm20) REVERT: A 463 ASN cc_start: 0.8840 (t0) cc_final: 0.8511 (t0) REVERT: A 557 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 692 GLU cc_start: 0.8515 (tp30) cc_final: 0.8308 (tp30) REVERT: A 743 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.6606 (t60) REVERT: A 844 MET cc_start: 0.8530 (mtm) cc_final: 0.7483 (tmt) REVERT: A 918 LYS cc_start: 0.8462 (mtmt) cc_final: 0.7920 (mmtt) REVERT: A 930 MET cc_start: 0.3267 (tpt) cc_final: 0.3051 (tpt) REVERT: A 1145 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 1149 GLU cc_start: 0.8091 (mp0) cc_final: 0.7760 (mp0) REVERT: A 1371 MET cc_start: 0.6450 (mmm) cc_final: 0.6161 (mmm) REVERT: B 122 MET cc_start: 0.8637 (mpp) cc_final: 0.8065 (mpp) REVERT: B 215 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7514 (ptp) REVERT: B 426 GLN cc_start: 0.4194 (OUTLIER) cc_final: 0.2600 (pm20) REVERT: B 463 ASN cc_start: 0.8958 (t0) cc_final: 0.8563 (t0) REVERT: B 488 MET cc_start: 0.8449 (tpt) cc_final: 0.8146 (tpt) REVERT: B 743 TRP cc_start: 0.8089 (OUTLIER) cc_final: 0.7002 (t60) REVERT: B 844 MET cc_start: 0.8740 (mtm) cc_final: 0.7745 (tmm) REVERT: B 857 MET cc_start: 0.5626 (tpt) cc_final: 0.5369 (tpt) REVERT: B 1145 GLU cc_start: 0.8401 (mp0) cc_final: 0.7821 (mp0) REVERT: B 1149 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: B 1156 ASP cc_start: 0.8362 (m-30) cc_final: 0.8127 (m-30) REVERT: B 1491 LEU cc_start: 0.8340 (mp) cc_final: 0.7758 (tp) REVERT: C 122 MET cc_start: 0.8164 (mpp) cc_final: 0.7369 (mpp) REVERT: C 215 MET cc_start: 0.7674 (mpp) cc_final: 0.7376 (mtt) REVERT: C 426 GLN cc_start: 0.3427 (OUTLIER) cc_final: 0.2724 (mm-40) REVERT: C 435 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8946 (pm20) REVERT: C 505 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8326 (mp0) REVERT: C 692 GLU cc_start: 0.8542 (tp30) cc_final: 0.8276 (tp30) REVERT: C 744 TRP cc_start: 0.8306 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: C 778 LEU cc_start: 0.7386 (mt) cc_final: 0.6846 (tp) REVERT: C 844 MET cc_start: 0.9108 (mtm) cc_final: 0.8555 (ptp) REVERT: C 923 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8825 (mmtt) REVERT: C 1122 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8222 (mt) REVERT: C 1325 LEU cc_start: 0.7294 (mm) cc_final: 0.7041 (mm) REVERT: C 1385 TRP cc_start: 0.7071 (m100) cc_final: 0.5854 (m100) REVERT: D 196 LYS cc_start: 0.8940 (tttm) cc_final: 0.8708 (tttm) REVERT: D 215 MET cc_start: 0.6754 (ptp) cc_final: 0.6379 (ptp) REVERT: D 501 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8145 (mtpp) REVERT: D 505 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: D 537 GLN cc_start: 0.9164 (tp40) cc_final: 0.8880 (mm-40) REVERT: D 726 ASP cc_start: 0.7403 (m-30) cc_final: 0.6715 (m-30) REVERT: D 743 TRP cc_start: 0.7578 (OUTLIER) cc_final: 0.6689 (t60) REVERT: D 760 MET cc_start: 0.8537 (ttt) cc_final: 0.8123 (ptm) REVERT: D 844 MET cc_start: 0.8994 (mtm) cc_final: 0.8204 (ptp) REVERT: D 911 MET cc_start: 0.8474 (mmm) cc_final: 0.8178 (mmm) REVERT: D 918 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7899 (mmtt) REVERT: D 1149 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7531 (mp0) REVERT: D 1489 LYS cc_start: 0.9338 (mtpt) cc_final: 0.9028 (mmmt) outliers start: 123 outliers final: 80 residues processed: 485 average time/residue: 0.5084 time to fit residues: 423.7051 Evaluate side-chains 455 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 360 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 743 TRP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 426 GLN Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 744 TRP Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 934 VAL Chi-restraints excluded: chain D residue 1151 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 2.9990 chunk 466 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 518 optimal weight: 30.0000 chunk 430 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 171 optimal weight: 8.9990 chunk 272 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 HIS ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1042 ASN D1058 HIS D1437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 41920 Z= 0.298 Angle : 0.690 12.965 57244 Z= 0.349 Chirality : 0.044 0.213 6580 Planarity : 0.005 0.060 7264 Dihedral : 6.923 59.146 6163 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.35 % Favored : 90.50 % Rotamer: Outliers : 3.98 % Allowed : 16.08 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5368 helix: 0.39 (0.11), residues: 2492 sheet: -0.39 (0.25), residues: 404 loop : -2.53 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 944 HIS 0.011 0.001 HIS B 559 PHE 0.022 0.001 PHE D 936 TYR 0.022 0.001 TYR C 833 ARG 0.006 0.000 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 398 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6784 (t0) REVERT: A 215 MET cc_start: 0.6952 (ptp) cc_final: 0.6541 (ptp) REVERT: A 404 LYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6343 (mmtp) REVERT: A 426 GLN cc_start: 0.3721 (OUTLIER) cc_final: 0.1567 (pm20) REVERT: A 463 ASN cc_start: 0.8953 (t0) cc_final: 0.8627 (t0) REVERT: A 557 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: A 692 GLU cc_start: 0.8587 (tp30) cc_final: 0.8360 (tp30) REVERT: A 743 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.6704 (t60) REVERT: A 844 MET cc_start: 0.8569 (mtm) cc_final: 0.7577 (tmt) REVERT: A 918 LYS cc_start: 0.8627 (mtmt) cc_final: 0.8060 (mmtt) REVERT: A 930 MET cc_start: 0.3354 (tpt) cc_final: 0.3151 (tpt) REVERT: A 1145 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8179 (mm-30) REVERT: A 1149 GLU cc_start: 0.8070 (mp0) cc_final: 0.7781 (mp0) REVERT: A 1371 MET cc_start: 0.6896 (mmm) cc_final: 0.6531 (mmm) REVERT: B 122 MET cc_start: 0.8670 (mpp) cc_final: 0.8051 (mpp) REVERT: B 196 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8414 (ttpp) REVERT: B 199 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8285 (pp30) REVERT: B 215 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7586 (ptp) REVERT: B 426 GLN cc_start: 0.4135 (OUTLIER) cc_final: 0.2582 (pm20) REVERT: B 430 ASP cc_start: 0.7483 (m-30) cc_final: 0.7102 (m-30) REVERT: B 463 ASN cc_start: 0.9018 (t0) cc_final: 0.8746 (t0) REVERT: B 488 MET cc_start: 0.8490 (tpt) cc_final: 0.8100 (tpt) REVERT: B 743 TRP cc_start: 0.8071 (OUTLIER) cc_final: 0.6897 (t60) REVERT: B 844 MET cc_start: 0.8748 (mtm) cc_final: 0.7654 (tmm) REVERT: B 857 MET cc_start: 0.5608 (tpt) cc_final: 0.5399 (tpt) REVERT: B 1156 ASP cc_start: 0.8416 (m-30) cc_final: 0.8147 (m-30) REVERT: B 1491 LEU cc_start: 0.8430 (mp) cc_final: 0.7825 (tp) REVERT: C 122 MET cc_start: 0.8293 (mpp) cc_final: 0.7644 (mpp) REVERT: C 215 MET cc_start: 0.7764 (mpp) cc_final: 0.7463 (mtt) REVERT: C 426 GLN cc_start: 0.3633 (OUTLIER) cc_final: 0.3014 (mm110) REVERT: C 435 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8966 (pm20) REVERT: C 505 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: C 743 TRP cc_start: 0.8039 (OUTLIER) cc_final: 0.6868 (t60) REVERT: C 744 TRP cc_start: 0.8417 (OUTLIER) cc_final: 0.8182 (m-10) REVERT: C 778 LEU cc_start: 0.7620 (mt) cc_final: 0.7100 (tp) REVERT: C 844 MET cc_start: 0.9078 (mtm) cc_final: 0.8561 (ptp) REVERT: C 911 MET cc_start: 0.8030 (mmm) cc_final: 0.7708 (mmp) REVERT: C 965 TRP cc_start: 0.5038 (m100) cc_final: 0.4633 (m100) REVERT: C 1149 GLU cc_start: 0.7993 (mp0) cc_final: 0.7605 (mp0) REVERT: D 215 MET cc_start: 0.6870 (ptp) cc_final: 0.6476 (ptp) REVERT: D 501 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8165 (mtpp) REVERT: D 699 GLU cc_start: 0.7953 (tp30) cc_final: 0.7748 (tp30) REVERT: D 743 TRP cc_start: 0.7649 (OUTLIER) cc_final: 0.6778 (t60) REVERT: D 844 MET cc_start: 0.8977 (mtm) cc_final: 0.8180 (ptp) REVERT: D 918 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7989 (mmtt) REVERT: D 1122 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8319 (mm) outliers start: 156 outliers final: 108 residues processed: 531 average time/residue: 0.5174 time to fit residues: 468.0545 Evaluate side-chains 489 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 366 time to evaluate : 4.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 743 TRP Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1346 HIS Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 426 GLN Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 743 TRP Chi-restraints excluded: chain C residue 744 TRP Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 730 VAL Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 835 TRP Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 934 VAL Chi-restraints excluded: chain D residue 1090 LEU Chi-restraints excluded: chain D residue 1122 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1243 ARG Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1477 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 378 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 436 optimal weight: 10.0000 chunk 289 optimal weight: 30.0000 chunk 516 optimal weight: 30.0000 chunk 323 optimal weight: 0.0020 chunk 314 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN B 953 GLN B1137 GLN ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41920 Z= 0.192 Angle : 0.646 14.989 57244 Z= 0.326 Chirality : 0.042 0.191 6580 Planarity : 0.004 0.058 7264 Dihedral : 6.782 57.120 6161 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.55 % Favored : 91.30 % Rotamer: Outliers : 3.16 % Allowed : 17.94 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5368 helix: 0.63 (0.11), residues: 2460 sheet: -0.34 (0.25), residues: 396 loop : -2.48 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1355 HIS 0.009 0.001 HIS B 559 PHE 0.021 0.001 PHE D 936 TYR 0.024 0.001 TYR C 833 ARG 0.006 0.000 ARG A 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 374 time to evaluate : 4.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.7614 (OUTLIER) cc_final: 0.7154 (t0) REVERT: A 215 MET cc_start: 0.6957 (ptp) cc_final: 0.6509 (ptp) REVERT: A 404 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6470 (mmtp) REVERT: A 420 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.2476 (tpp-160) REVERT: A 426 GLN cc_start: 0.3699 (OUTLIER) cc_final: 0.1542 (pm20) REVERT: A 463 ASN cc_start: 0.8924 (t0) cc_final: 0.8557 (t0) REVERT: A 557 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: A 692 GLU cc_start: 0.8525 (tp30) cc_final: 0.8315 (tp30) REVERT: A 743 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.6807 (t60) REVERT: A 844 MET cc_start: 0.8552 (mtm) cc_final: 0.7561 (tmt) REVERT: A 930 MET cc_start: 0.3267 (tpt) cc_final: 0.3051 (tpt) REVERT: A 1149 GLU cc_start: 0.8034 (mp0) cc_final: 0.7749 (mp0) REVERT: A 1371 MET cc_start: 0.6918 (mmm) cc_final: 0.6548 (mmm) REVERT: B 122 MET cc_start: 0.8665 (mpp) cc_final: 0.8054 (mpp) REVERT: B 196 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8363 (ttpp) REVERT: B 199 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8260 (pp30) REVERT: B 215 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7597 (ptp) REVERT: B 426 GLN cc_start: 0.4039 (OUTLIER) cc_final: 0.2557 (pm20) REVERT: B 430 ASP cc_start: 0.7404 (m-30) cc_final: 0.7051 (m-30) REVERT: B 463 ASN cc_start: 0.8973 (t0) cc_final: 0.8676 (t0) REVERT: B 488 MET cc_start: 0.8448 (tpt) cc_final: 0.8146 (tpt) REVERT: B 697 ASP cc_start: 0.8183 (t0) cc_final: 0.7632 (t0) REVERT: B 743 TRP cc_start: 0.8025 (OUTLIER) cc_final: 0.6944 (t60) REVERT: B 844 MET cc_start: 0.8739 (mtm) cc_final: 0.7636 (tmm) REVERT: B 857 MET cc_start: 0.5612 (tpt) cc_final: 0.5274 (tpt) REVERT: B 1156 ASP cc_start: 0.8386 (m-30) cc_final: 0.8124 (m-30) REVERT: B 1158 MET cc_start: 0.8749 (mmp) cc_final: 0.8469 (mmp) REVERT: B 1491 LEU cc_start: 0.8387 (mp) cc_final: 0.7829 (tp) REVERT: C 122 MET cc_start: 0.8279 (mpp) cc_final: 0.7567 (mpp) REVERT: C 215 MET cc_start: 0.7783 (mpp) cc_final: 0.7449 (mtt) REVERT: C 426 GLN cc_start: 0.3499 (OUTLIER) cc_final: 0.2946 (mm110) REVERT: C 435 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8948 (pm20) REVERT: C 505 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: C 558 MET cc_start: 0.8811 (mmm) cc_final: 0.8247 (mmt) REVERT: C 692 GLU cc_start: 0.8512 (tp30) cc_final: 0.8268 (tp30) REVERT: C 743 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.6910 (t60) REVERT: C 778 LEU cc_start: 0.7505 (mt) cc_final: 0.6992 (tp) REVERT: C 844 MET cc_start: 0.9033 (mtm) cc_final: 0.8173 (tmm) REVERT: C 911 MET cc_start: 0.8009 (mmm) cc_final: 0.7699 (mmp) REVERT: C 1149 GLU cc_start: 0.8114 (mp0) cc_final: 0.7381 (mp0) REVERT: D 196 LYS cc_start: 0.8996 (tttt) cc_final: 0.8795 (tttm) REVERT: D 215 MET cc_start: 0.6896 (ptp) cc_final: 0.6473 (ptp) REVERT: D 483 ASP cc_start: 0.8295 (t0) cc_final: 0.7982 (t0) REVERT: D 501 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8184 (mtpp) REVERT: D 537 GLN cc_start: 0.9187 (tp40) cc_final: 0.8983 (mm-40) REVERT: D 699 GLU cc_start: 0.7898 (tp30) cc_final: 0.7671 (tp30) REVERT: D 743 TRP cc_start: 0.7671 (OUTLIER) cc_final: 0.6832 (t60) REVERT: D 844 MET cc_start: 0.8941 (mtm) cc_final: 0.8100 (ptp) REVERT: D 868 TRP cc_start: 0.6308 (m100) cc_final: 0.5762 (m100) REVERT: D 911 MET cc_start: 0.8307 (mmm) cc_final: 0.7959 (mmm) REVERT: D 916 ILE cc_start: 0.8207 (tp) cc_final: 0.7970 (tp) REVERT: D 918 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7931 (mmtt) REVERT: D 1149 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7837 (mp0) outliers start: 124 outliers final: 87 residues processed: 478 average time/residue: 0.5042 time to fit residues: 412.1775 Evaluate side-chains 461 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 360 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 743 TRP Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 426 GLN Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 743 TRP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1355 TRP Chi-restraints excluded: chain D residue 1477 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 101 optimal weight: 0.0270 chunk 100 optimal weight: 6.9990 chunk 328 optimal weight: 0.8980 chunk 351 optimal weight: 20.0000 chunk 255 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 406 optimal weight: 40.0000 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 GLN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1450 GLN D 426 GLN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41920 Z= 0.210 Angle : 0.652 13.711 57244 Z= 0.327 Chirality : 0.042 0.280 6580 Planarity : 0.004 0.057 7264 Dihedral : 6.663 55.535 6161 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.04 % Favored : 90.85 % Rotamer: Outliers : 3.29 % Allowed : 18.35 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5368 helix: 0.73 (0.11), residues: 2460 sheet: -0.35 (0.25), residues: 396 loop : -2.44 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 944 HIS 0.009 0.001 HIS B 559 PHE 0.019 0.001 PHE D 936 TYR 0.022 0.001 TYR C 833 ARG 0.010 0.000 ARG D 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 381 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.6976 (t0) REVERT: A 215 MET cc_start: 0.7016 (ptp) cc_final: 0.6576 (ptp) REVERT: A 404 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6424 (mmtp) REVERT: A 420 ARG cc_start: 0.4833 (OUTLIER) cc_final: 0.2443 (tpp-160) REVERT: A 426 GLN cc_start: 0.3765 (OUTLIER) cc_final: 0.1598 (pm20) REVERT: A 463 ASN cc_start: 0.8937 (t0) cc_final: 0.8579 (t0) REVERT: A 505 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: A 557 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: A 692 GLU cc_start: 0.8550 (tp30) cc_final: 0.8285 (tp30) REVERT: A 743 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.6805 (t60) REVERT: A 844 MET cc_start: 0.8553 (mtm) cc_final: 0.7592 (tmt) REVERT: A 1149 GLU cc_start: 0.8054 (mp0) cc_final: 0.7760 (mp0) REVERT: A 1371 MET cc_start: 0.6969 (mmm) cc_final: 0.6601 (mmm) REVERT: B 122 MET cc_start: 0.8640 (mpp) cc_final: 0.8043 (mpp) REVERT: B 196 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8396 (ttpt) REVERT: B 199 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8222 (pp30) REVERT: B 215 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7598 (ptp) REVERT: B 426 GLN cc_start: 0.3997 (OUTLIER) cc_final: 0.2554 (pm20) REVERT: B 463 ASN cc_start: 0.8993 (t0) cc_final: 0.8699 (t0) REVERT: B 488 MET cc_start: 0.8455 (tpt) cc_final: 0.8134 (tpt) REVERT: B 743 TRP cc_start: 0.8027 (OUTLIER) cc_final: 0.6873 (t60) REVERT: B 844 MET cc_start: 0.8738 (mtm) cc_final: 0.7636 (tmm) REVERT: B 857 MET cc_start: 0.5666 (tpt) cc_final: 0.5345 (tpt) REVERT: B 1156 ASP cc_start: 0.8404 (m-30) cc_final: 0.8149 (m-30) REVERT: B 1158 MET cc_start: 0.8786 (mmp) cc_final: 0.8490 (mmp) REVERT: B 1491 LEU cc_start: 0.8460 (mp) cc_final: 0.7915 (tp) REVERT: C 122 MET cc_start: 0.8284 (mpp) cc_final: 0.7566 (mpp) REVERT: C 215 MET cc_start: 0.7784 (mpp) cc_final: 0.7449 (mtt) REVERT: C 426 GLN cc_start: 0.3536 (OUTLIER) cc_final: 0.2983 (mm110) REVERT: C 435 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8911 (pm20) REVERT: C 505 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8310 (mp0) REVERT: C 558 MET cc_start: 0.8830 (mmm) cc_final: 0.8281 (mmt) REVERT: C 692 GLU cc_start: 0.8531 (tp30) cc_final: 0.8095 (tp30) REVERT: C 743 TRP cc_start: 0.8011 (OUTLIER) cc_final: 0.6932 (t60) REVERT: C 778 LEU cc_start: 0.7425 (mt) cc_final: 0.6937 (tp) REVERT: C 844 MET cc_start: 0.9032 (mtm) cc_final: 0.8459 (ptp) REVERT: C 965 TRP cc_start: 0.5057 (m100) cc_final: 0.4721 (m100) REVERT: C 1149 GLU cc_start: 0.8061 (mp0) cc_final: 0.7718 (mp0) REVERT: C 1158 MET cc_start: 0.8896 (mmp) cc_final: 0.8539 (mmt) REVERT: D 215 MET cc_start: 0.6976 (ptp) cc_final: 0.6496 (ptp) REVERT: D 483 ASP cc_start: 0.8230 (t0) cc_final: 0.8018 (t0) REVERT: D 501 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8351 (mtpp) REVERT: D 699 GLU cc_start: 0.7895 (tp30) cc_final: 0.7655 (tp30) REVERT: D 723 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: D 743 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6851 (t60) REVERT: D 844 MET cc_start: 0.8949 (mtm) cc_final: 0.8088 (ptp) REVERT: D 868 TRP cc_start: 0.6306 (m100) cc_final: 0.5951 (m100) REVERT: D 923 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8721 (mttt) REVERT: D 1149 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7823 (mp0) outliers start: 129 outliers final: 97 residues processed: 488 average time/residue: 0.5020 time to fit residues: 418.0631 Evaluate side-chains 475 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 362 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 557 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 743 TRP Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 918 LYS Chi-restraints excluded: chain B residue 925 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1090 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1346 HIS Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 426 GLN Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 743 TRP Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 704 LEU Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 1090 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1243 ARG Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1477 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 5.9990 chunk 494 optimal weight: 7.9990 chunk 451 optimal weight: 6.9990 chunk 481 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 378 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 435 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 479 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 211 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 HIS A1437 ASN B 346 ASN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN B1450 GLN C 156 HIS C 168 ASN ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1437 ASN D 168 ASN D 280 ASN D 414 GLN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 GLN ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 41920 Z= 0.478 Angle : 0.818 11.493 57244 Z= 0.416 Chirality : 0.048 0.262 6580 Planarity : 0.006 0.059 7264 Dihedral : 7.058 56.213 6161 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.15 % Favored : 89.72 % Rotamer: Outliers : 3.62 % Allowed : 18.43 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.38 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5368 helix: 0.25 (0.10), residues: 2512 sheet: -0.64 (0.24), residues: 404 loop : -2.53 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 944 HIS 0.011 0.002 HIS A 684 PHE 0.029 0.002 PHE C 948 TYR 0.033 0.002 TYR C 682 ARG 0.008 0.001 ARG D 623 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 367 time to evaluate : 4.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.6831 (t0) REVERT: A 215 MET cc_start: 0.7186 (ptp) cc_final: 0.6878 (ptp) REVERT: A 420 ARG cc_start: 0.5155 (OUTLIER) cc_final: 0.3818 (tpp-160) REVERT: A 426 GLN cc_start: 0.3544 (OUTLIER) cc_final: 0.2991 (mm110) REVERT: A 463 ASN cc_start: 0.9057 (t0) cc_final: 0.8781 (t0) REVERT: A 623 ARG cc_start: 0.7153 (mpp-170) cc_final: 0.6883 (mpt180) REVERT: A 699 GLU cc_start: 0.8087 (tp30) cc_final: 0.7727 (tp30) REVERT: A 743 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.6956 (t60) REVERT: A 844 MET cc_start: 0.8597 (mtm) cc_final: 0.7639 (tmt) REVERT: A 903 PHE cc_start: 0.6037 (OUTLIER) cc_final: 0.5422 (t80) REVERT: A 1118 GLU cc_start: 0.7998 (tp30) cc_final: 0.7040 (tp30) REVERT: A 1149 GLU cc_start: 0.8033 (mp0) cc_final: 0.7696 (mp0) REVERT: A 1158 MET cc_start: 0.8449 (mmt) cc_final: 0.8018 (mmp) REVERT: A 1371 MET cc_start: 0.7022 (mmm) cc_final: 0.6572 (mmm) REVERT: A 1385 TRP cc_start: 0.6621 (m100) cc_final: 0.6017 (m100) REVERT: B 122 MET cc_start: 0.8757 (mpp) cc_final: 0.8129 (mpp) REVERT: B 215 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7544 (ptp) REVERT: B 295 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6044 (m-10) REVERT: B 420 ARG cc_start: 0.4681 (OUTLIER) cc_final: 0.2641 (tpp-160) REVERT: B 426 GLN cc_start: 0.4138 (OUTLIER) cc_final: 0.2475 (pm20) REVERT: B 463 ASN cc_start: 0.9097 (t0) cc_final: 0.8856 (t0) REVERT: B 743 TRP cc_start: 0.8222 (OUTLIER) cc_final: 0.7253 (t60) REVERT: B 844 MET cc_start: 0.8801 (mtm) cc_final: 0.7691 (tmm) REVERT: B 857 MET cc_start: 0.5740 (tpt) cc_final: 0.5400 (tpt) REVERT: B 1156 ASP cc_start: 0.8601 (m-30) cc_final: 0.8399 (m-30) REVERT: B 1158 MET cc_start: 0.8902 (mmp) cc_final: 0.8495 (mmp) REVERT: B 1351 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.3201 (ttp) REVERT: B 1491 LEU cc_start: 0.8682 (mp) cc_final: 0.8233 (tp) REVERT: C 122 MET cc_start: 0.8534 (mpp) cc_final: 0.8069 (mpp) REVERT: C 168 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7014 (t0) REVERT: C 196 LYS cc_start: 0.9035 (tttm) cc_final: 0.8815 (tttm) REVERT: C 426 GLN cc_start: 0.3521 (OUTLIER) cc_final: 0.2918 (mm110) REVERT: C 435 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8956 (pm20) REVERT: C 505 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: C 743 TRP cc_start: 0.8092 (OUTLIER) cc_final: 0.6948 (t60) REVERT: C 778 LEU cc_start: 0.7775 (mt) cc_final: 0.7305 (tp) REVERT: C 844 MET cc_start: 0.9047 (mtm) cc_final: 0.8524 (ptp) REVERT: C 948 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.5887 (t80) REVERT: C 1149 GLU cc_start: 0.8065 (mp0) cc_final: 0.7212 (mp0) REVERT: C 1158 MET cc_start: 0.8868 (mmp) cc_final: 0.8507 (mmp) REVERT: D 168 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7031 (t0) REVERT: D 196 LYS cc_start: 0.8966 (tttt) cc_final: 0.8741 (ttpp) REVERT: D 215 MET cc_start: 0.7084 (ptp) cc_final: 0.6740 (ptp) REVERT: D 430 ASP cc_start: 0.7090 (m-30) cc_final: 0.6658 (m-30) REVERT: D 505 GLU cc_start: 0.8186 (mp0) cc_final: 0.7969 (mp0) REVERT: D 699 GLU cc_start: 0.8016 (tp30) cc_final: 0.7770 (tp30) REVERT: D 723 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: D 743 TRP cc_start: 0.7883 (OUTLIER) cc_final: 0.7050 (t60) REVERT: D 844 MET cc_start: 0.8986 (mtm) cc_final: 0.8315 (ptt) REVERT: D 923 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8725 (mtpt) REVERT: D 930 MET cc_start: 0.3625 (tpt) cc_final: 0.3125 (tpt) REVERT: D 1149 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7814 (mp0) outliers start: 142 outliers final: 103 residues processed: 496 average time/residue: 0.5027 time to fit residues: 427.2725 Evaluate side-chains 467 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 344 time to evaluate : 4.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 730 VAL Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1477 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 420 ARG Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 743 TRP Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1090 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1346 HIS Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 276 CYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 426 GLN Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 743 TRP Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 730 VAL Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 813 PHE Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1090 LEU Chi-restraints excluded: chain D residue 1138 PHE Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1243 ARG Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 0.9990 chunk 509 optimal weight: 9.9990 chunk 310 optimal weight: 0.1980 chunk 241 optimal weight: 0.3980 chunk 353 optimal weight: 3.9990 chunk 533 optimal weight: 9.9990 chunk 491 optimal weight: 10.0000 chunk 425 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 444 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN C 444 GLN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 GLN D 463 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1056 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41920 Z= 0.191 Angle : 0.690 16.621 57244 Z= 0.347 Chirality : 0.043 0.274 6580 Planarity : 0.005 0.058 7264 Dihedral : 6.805 54.625 6159 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.77 % Favored : 91.15 % Rotamer: Outliers : 2.57 % Allowed : 19.90 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 5368 helix: 0.73 (0.11), residues: 2472 sheet: -0.51 (0.24), residues: 396 loop : -2.46 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 944 HIS 0.010 0.001 HIS B 559 PHE 0.019 0.001 PHE B 690 TYR 0.020 0.001 TYR C 833 ARG 0.014 0.001 ARG C 581 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10736 Ramachandran restraints generated. 5368 Oldfield, 0 Emsley, 5368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 367 time to evaluate : 5.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6530 (t0) REVERT: A 215 MET cc_start: 0.7118 (ptp) cc_final: 0.6629 (ptp) REVERT: A 420 ARG cc_start: 0.4984 (OUTLIER) cc_final: 0.3651 (tpp-160) REVERT: A 426 GLN cc_start: 0.3607 (OUTLIER) cc_final: 0.1464 (pm20) REVERT: A 463 ASN cc_start: 0.8937 (t0) cc_final: 0.8650 (t0) REVERT: A 505 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: A 692 GLU cc_start: 0.8473 (tp30) cc_final: 0.8164 (tp30) REVERT: A 743 TRP cc_start: 0.7857 (OUTLIER) cc_final: 0.6908 (t60) REVERT: A 844 MET cc_start: 0.8580 (mtm) cc_final: 0.7604 (tmt) REVERT: A 1149 GLU cc_start: 0.7995 (mp0) cc_final: 0.7703 (mp0) REVERT: A 1371 MET cc_start: 0.6960 (mmm) cc_final: 0.6500 (mmm) REVERT: B 122 MET cc_start: 0.8744 (mpp) cc_final: 0.8493 (mpp) REVERT: B 196 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8358 (ttpp) REVERT: B 199 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8323 (pp30) REVERT: B 215 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7492 (ptp) REVERT: B 426 GLN cc_start: 0.4146 (OUTLIER) cc_final: 0.2571 (pm20) REVERT: B 435 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8751 (pm20) REVERT: B 463 ASN cc_start: 0.8999 (t0) cc_final: 0.8672 (t0) REVERT: B 488 MET cc_start: 0.8491 (tpt) cc_final: 0.8237 (tpt) REVERT: B 697 ASP cc_start: 0.8147 (t0) cc_final: 0.7655 (t0) REVERT: B 743 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.6776 (t60) REVERT: B 778 LEU cc_start: 0.7690 (mt) cc_final: 0.6970 (tt) REVERT: B 844 MET cc_start: 0.8776 (mtm) cc_final: 0.7659 (tmm) REVERT: B 857 MET cc_start: 0.5761 (tpt) cc_final: 0.5424 (tpt) REVERT: B 1117 GLU cc_start: 0.7953 (tp30) cc_final: 0.7750 (tp30) REVERT: B 1156 ASP cc_start: 0.8509 (m-30) cc_final: 0.8299 (m-30) REVERT: B 1158 MET cc_start: 0.8860 (mmp) cc_final: 0.8553 (mmp) REVERT: B 1351 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.3446 (ttp) REVERT: B 1491 LEU cc_start: 0.8647 (mp) cc_final: 0.8214 (tp) REVERT: C 122 MET cc_start: 0.8513 (mpp) cc_final: 0.8027 (mpp) REVERT: C 135 LEU cc_start: 0.7879 (mm) cc_final: 0.7607 (tp) REVERT: C 426 GLN cc_start: 0.3667 (OUTLIER) cc_final: 0.3131 (mm110) REVERT: C 435 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (pm20) REVERT: C 505 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: C 743 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.6777 (t60) REVERT: C 778 LEU cc_start: 0.7447 (mt) cc_final: 0.6946 (tp) REVERT: C 844 MET cc_start: 0.9042 (mtm) cc_final: 0.8071 (tmm) REVERT: C 911 MET cc_start: 0.8023 (mmm) cc_final: 0.7709 (mmp) REVERT: C 923 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8525 (mmtp) REVERT: C 1149 GLU cc_start: 0.7991 (mp0) cc_final: 0.7597 (mp0) REVERT: C 1158 MET cc_start: 0.8872 (mmp) cc_final: 0.8539 (mmp) REVERT: D 196 LYS cc_start: 0.9002 (tttt) cc_final: 0.8764 (ttpp) REVERT: D 215 MET cc_start: 0.7011 (ptp) cc_final: 0.6662 (ptp) REVERT: D 430 ASP cc_start: 0.7311 (m-30) cc_final: 0.6820 (m-30) REVERT: D 444 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: D 483 ASP cc_start: 0.8232 (t0) cc_final: 0.7979 (t0) REVERT: D 699 GLU cc_start: 0.7847 (tp30) cc_final: 0.7568 (tp30) REVERT: D 723 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: D 743 TRP cc_start: 0.7664 (OUTLIER) cc_final: 0.6928 (t60) REVERT: D 844 MET cc_start: 0.8937 (mtm) cc_final: 0.8187 (ptp) REVERT: D 923 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8663 (mtpt) REVERT: D 930 MET cc_start: 0.3636 (tpt) cc_final: 0.3193 (tpt) REVERT: D 1158 MET cc_start: 0.8903 (mmm) cc_final: 0.8655 (mmp) outliers start: 101 outliers final: 77 residues processed: 458 average time/residue: 0.5109 time to fit residues: 397.6296 Evaluate side-chains 449 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 355 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 687 ILE Chi-restraints excluded: chain B residue 704 LEU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 743 TRP Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 929 ARG Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1090 LEU Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1270 ILE Chi-restraints excluded: chain B residue 1346 HIS Chi-restraints excluded: chain B residue 1351 MET Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 426 GLN Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 743 TRP Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 929 ARG Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1270 ILE Chi-restraints excluded: chain C residue 1477 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 602 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 648 CYS Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 918 LYS Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1090 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 0.8980 chunk 452 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 392 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 118 optimal weight: 40.0000 chunk 425 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 437 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 444 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 912 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.185890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121589 restraints weight = 89832.781| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 4.32 r_work: 0.3583 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.355 41920 Z= 0.342 Angle : 0.801 59.196 57244 Z= 0.436 Chirality : 0.044 0.581 6580 Planarity : 0.005 0.147 7264 Dihedral : 6.800 54.618 6159 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.74 % Favored : 91.19 % Rotamer: Outliers : 2.68 % Allowed : 20.13 % Favored : 77.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.11), residues: 5368 helix: 0.73 (0.11), residues: 2472 sheet: -0.51 (0.24), residues: 396 loop : -2.46 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 868 HIS 0.034 0.001 HIS D 912 PHE 0.025 0.001 PHE A 914 TYR 0.020 0.001 TYR C 833 ARG 0.010 0.000 ARG C 581 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9617.87 seconds wall clock time: 176 minutes 0.33 seconds (10560.33 seconds total)