Starting phenix.real_space_refine on Tue Aug 26 21:01:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e6q_27922/08_2025/8e6q_27922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e6q_27922/08_2025/8e6q_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e6q_27922/08_2025/8e6q_27922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e6q_27922/08_2025/8e6q_27922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e6q_27922/08_2025/8e6q_27922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e6q_27922/08_2025/8e6q_27922.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'GLU:plan': 35, 'PHE:plan': 7, 'ASP:plan': 20, 'HIS:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 2} 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, 'GLU:plan': 35, 'PHE:plan': 7, 'ASP:plan': 20, 'HIS:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 2} 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, 'GLU:plan': 35, 'PHE:plan': 7, 'ASP:plan': 20, 'HIS:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 2} 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, 'GLU:plan': 35, 'PHE:plan': 7, 'ASP:plan': 20, 'HIS:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 2} 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: 9.82, per 1000 atoms: 0.24 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: 3.79 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.50 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: 9.87 Time building geometry restraints manager: 5.10 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: 0.13 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: 1.870 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: 0.050 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 40.990 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.110 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- 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= 0.179 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 : 12.50 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.001 ARG C 442 TYR 0.015 0.001 TYR C 155 PHE 0.013 0.001 PHE C 773 TRP 0.019 0.001 TRP D 743 HIS 0.007 0.001 HIS D1502 Details of bonding type rmsd covalent geometry : bond 0.00378 (41920) covalent geometry : angle 0.86097 (57244) hydrogen bonds : bond 0.23124 ( 1710) hydrogen bonds : angle 7.04762 ( 4926) *********************** 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 : 1.631 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: 0.6635 (mt) REVERT: A 669 THR cc_start: 0.7051 (t) cc_final: 0.6803 (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: 0.7758 (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: 0.7856 (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: 0.7896 (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: 0.7743 (m-30) REVERT: B 1351 MET cc_start: 0.1721 (ttm) cc_final: 0.1330 (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: 0.5481 (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: 0.8463 (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: 0.8517 (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: 0.2494 time to fit residues: 288.0434 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 : 1.524 ------------------------------------------------------------------------------- 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 394 optimal weight: 50.0000 chunk 430 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 40.0000 chunk 414 optimal weight: 50.0000 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 444 GLN A 446 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 751 ASN A 912 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1437 ASN B 168 ASN B 271 GLN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN B 912 HIS ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1042 ASN B1502 HIS ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS C 338 HIS ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 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 338 HIS D 444 GLN D 446 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 D 732 HIS D 912 HIS ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1042 ASN D1437 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.186575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.121370 restraints weight = 90641.833| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 4.88 r_work: 0.3540 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 41920 Z= 0.356 Angle : 0.937 11.396 57244 Z= 0.477 Chirality : 0.052 0.294 6580 Planarity : 0.007 0.102 7264 Dihedral : 10.306 92.577 6222 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.87 % Favored : 89.92 % Rotamer: Outliers : 2.88 % Allowed : 9.96 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.38 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.11), residues: 5368 helix: -0.75 (0.10), residues: 2448 sheet: -0.51 (0.27), residues: 372 loop : -2.76 (0.11), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 962 TYR 0.030 0.002 TYR A 833 PHE 0.032 0.003 PHE B 948 TRP 0.055 0.004 TRP D 868 HIS 0.026 0.002 HIS C 912 Details of bonding type rmsd covalent geometry : bond 0.00829 (41920) covalent geometry : angle 0.93698 (57244) hydrogen bonds : bond 0.06109 ( 1710) hydrogen bonds : angle 5.50506 ( 4926) *********************** 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 564 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 451 time to evaluate : 1.543 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 122 MET cc_start: 0.8158 (mpp) cc_final: 0.7776 (mpp) REVERT: A 168 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.6951 (t0) REVERT: A 215 MET cc_start: 0.6097 (ptp) cc_final: 0.5847 (ptp) REVERT: A 680 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8309 (tm-30) REVERT: A 699 GLU cc_start: 0.8780 (tp30) cc_final: 0.8446 (tp30) REVERT: A 743 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.6691 (t60) REVERT: A 844 MET cc_start: 0.8388 (mtm) cc_final: 0.7527 (tmm) REVERT: A 868 TRP cc_start: 0.6282 (m100) cc_final: 0.5717 (m100) REVERT: A 886 ARG cc_start: 0.6226 (tmt-80) cc_final: 0.5708 (tpp-160) REVERT: A 912 HIS cc_start: 0.8368 (t70) cc_final: 0.7977 (t70) REVERT: A 918 LYS cc_start: 0.8359 (mtmt) cc_final: 0.7813 (mmtt) REVERT: A 1137 GLN cc_start: 0.8911 (tp40) cc_final: 0.8426 (tm-30) REVERT: A 1484 LEU cc_start: 0.8303 (tp) cc_final: 0.7896 (tp) REVERT: B 122 MET cc_start: 0.8838 (mpp) cc_final: 0.8237 (mpp) REVERT: B 168 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7274 (t0) REVERT: B 215 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7086 (ptp) REVERT: B 295 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.6287 (m-10) REVERT: B 483 ASP cc_start: 0.8702 (t70) cc_final: 0.8335 (m-30) REVERT: B 692 GLU cc_start: 0.9278 (tp30) cc_final: 0.9066 (tp30) REVERT: B 844 MET cc_start: 0.8655 (mtm) cc_final: 0.7729 (tmm) REVERT: B 857 MET cc_start: 0.5451 (tpt) cc_final: 0.5192 (tpt) REVERT: B 868 TRP cc_start: 0.6152 (m100) cc_final: 0.5817 (m100) REVERT: B 912 HIS cc_start: 0.7864 (t70) cc_final: 0.7436 (t-170) REVERT: B 1149 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: B 1351 MET cc_start: 0.1794 (ttm) cc_final: 0.1572 (mpp) REVERT: B 1484 LEU cc_start: 0.8240 (tp) cc_final: 0.7764 (tp) REVERT: C 122 MET cc_start: 0.8193 (mpp) cc_final: 0.7541 (mpp) REVERT: C 215 MET cc_start: 0.7230 (mpp) cc_final: 0.6880 (mtt) REVERT: C 505 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8640 (mp0) REVERT: C 571 ASP cc_start: 0.7692 (m-30) cc_final: 0.7274 (p0) REVERT: C 692 GLU cc_start: 0.9344 (tp30) cc_final: 0.8777 (tp30) REVERT: C 699 GLU cc_start: 0.8631 (tp30) cc_final: 0.8410 (tp30) REVERT: C 843 GLU cc_start: 0.8017 (mp0) cc_final: 0.7718 (mp0) REVERT: C 844 MET cc_start: 0.9103 (mtm) cc_final: 0.8568 (ptp) REVERT: C 911 MET cc_start: 0.7982 (mmp) cc_final: 0.7561 (mmm) REVERT: C 918 LYS cc_start: 0.8658 (mptt) cc_final: 0.8363 (mmtt) REVERT: C 1385 TRP cc_start: 0.6426 (m100) cc_final: 0.5405 (m100) REVERT: D 215 MET cc_start: 0.6441 (ptp) cc_final: 0.6231 (ptp) REVERT: D 571 ASP cc_start: 0.7737 (m-30) cc_final: 0.7514 (p0) REVERT: D 665 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8893 (tm-30) REVERT: D 673 GLU cc_start: 0.8872 (tt0) cc_final: 0.8611 (tt0) REVERT: D 680 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8274 (tm-30) REVERT: D 743 TRP cc_start: 0.7480 (OUTLIER) cc_final: 0.6617 (t60) REVERT: D 844 MET cc_start: 0.8965 (mtm) cc_final: 0.8298 (ptp) REVERT: D 911 MET cc_start: 0.8546 (mmp) cc_final: 0.8071 (mmm) REVERT: D 918 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7823 (mmtt) outliers start: 113 outliers final: 59 residues processed: 531 average time/residue: 0.2392 time to fit residues: 211.8152 Evaluate side-chains 441 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 374 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 195 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 465 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 743 TRP Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 168 ASN 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 313 THR 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 520 LEU 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 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 295 TYR 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 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 925 ILE Chi-restraints excluded: chain C residue 1090 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1149 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 435 GLN Chi-restraints excluded: chain D residue 731 SER Chi-restraints excluded: chain D residue 743 TRP 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 903 PHE Chi-restraints excluded: chain D residue 1123 SER 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 345 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 518 optimal weight: 30.0000 chunk 165 optimal weight: 40.0000 chunk 374 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 477 optimal weight: 6.9990 chunk 492 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 381 optimal weight: 0.0980 chunk 5 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 346 ASN A 495 ASN A 557 GLN A 560 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1089 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 280 ASN B 444 GLN B 557 GLN B 560 HIS ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1346 HIS ** C 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 GLN ** 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 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 557 GLN D 646 GLN ** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.191204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.128338 restraints weight = 90373.142| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 4.39 r_work: 0.3687 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41920 Z= 0.132 Angle : 0.672 9.952 57244 Z= 0.341 Chirality : 0.043 0.243 6580 Planarity : 0.005 0.070 7264 Dihedral : 8.581 73.479 6168 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.23 % Favored : 91.58 % Rotamer: Outliers : 2.19 % Allowed : 13.56 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.11), residues: 5368 helix: -0.11 (0.10), residues: 2468 sheet: -0.42 (0.27), residues: 372 loop : -2.65 (0.11), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 787 TYR 0.031 0.001 TYR B 833 PHE 0.026 0.001 PHE C 937 TRP 0.028 0.002 TRP D 743 HIS 0.010 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00285 (41920) covalent geometry : angle 0.67196 (57244) hydrogen bonds : bond 0.04483 ( 1710) hydrogen bonds : angle 4.82107 ( 4926) *********************** 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 514 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 428 time to evaluate : 1.532 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: 0.5921 (ptp) cc_final: 0.5644 (ptp) REVERT: A 404 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.6160 (mmtp) REVERT: A 488 MET cc_start: 0.8432 (tpt) cc_final: 0.7959 (tpt) REVERT: A 521 TYR cc_start: 0.8876 (t80) cc_final: 0.8670 (t80) REVERT: A 680 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8231 (tm-30) REVERT: A 727 MET cc_start: 0.8451 (mmt) cc_final: 0.8100 (mmm) REVERT: A 728 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8805 (mtmt) REVERT: A 760 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8178 (ptm) REVERT: A 844 MET cc_start: 0.8506 (mtm) cc_final: 0.7421 (tmm) REVERT: A 868 TRP cc_start: 0.6241 (m100) cc_final: 0.5649 (m100) REVERT: A 912 HIS cc_start: 0.8298 (t70) cc_final: 0.7918 (t70) REVERT: A 918 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7661 (mmtt) REVERT: A 930 MET cc_start: 0.3818 (tpt) cc_final: 0.3506 (tpt) REVERT: A 1047 MET cc_start: 0.5642 (ppp) cc_final: 0.5439 (ppp) REVERT: A 1125 GLU cc_start: 0.8726 (tt0) cc_final: 0.8518 (tt0) REVERT: B 122 MET cc_start: 0.8854 (mpp) cc_final: 0.8270 (mpp) REVERT: B 168 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7300 (t0) REVERT: B 196 LYS cc_start: 0.8729 (tttt) cc_final: 0.8492 (ttpt) REVERT: B 199 GLN cc_start: 0.8279 (pp30) cc_final: 0.7992 (pp30) REVERT: B 215 MET cc_start: 0.7265 (ptp) cc_final: 0.7037 (ptp) REVERT: B 444 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7895 (pp30) REVERT: B 463 ASN cc_start: 0.9155 (t0) cc_final: 0.8827 (t0) REVERT: B 488 MET cc_start: 0.8440 (tpt) cc_final: 0.8214 (tpt) REVERT: B 844 MET cc_start: 0.8691 (mtm) cc_final: 0.7750 (tmm) REVERT: B 857 MET cc_start: 0.5439 (tpt) cc_final: 0.5158 (tpt) REVERT: B 868 TRP cc_start: 0.6172 (m100) cc_final: 0.5946 (m100) REVERT: B 965 TRP cc_start: 0.4691 (m100) cc_final: 0.4382 (m100) REVERT: B 1145 GLU cc_start: 0.8837 (mp0) cc_final: 0.8167 (mp0) REVERT: B 1149 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: C 122 MET cc_start: 0.8174 (mpp) cc_final: 0.7446 (mpp) REVERT: C 215 MET cc_start: 0.7363 (mpp) cc_final: 0.6987 (mtt) REVERT: C 505 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: C 558 MET cc_start: 0.8818 (mmm) cc_final: 0.8096 (mmt) REVERT: C 565 LEU cc_start: 0.8256 (mt) cc_final: 0.7155 (mp) REVERT: C 571 ASP cc_start: 0.7276 (m-30) cc_final: 0.7016 (p0) REVERT: C 692 GLU cc_start: 0.9238 (tp30) cc_final: 0.8829 (tp30) REVERT: C 699 GLU cc_start: 0.8304 (tp30) cc_final: 0.8093 (tp30) REVERT: C 778 LEU cc_start: 0.8272 (mt) cc_final: 0.7671 (tp) REVERT: C 835 TRP cc_start: 0.3823 (t-100) cc_final: 0.2972 (t-100) REVERT: C 844 MET cc_start: 0.9139 (mtm) cc_final: 0.8568 (ptp) REVERT: C 911 MET cc_start: 0.7878 (mmp) cc_final: 0.7518 (mmm) REVERT: C 918 LYS cc_start: 0.8656 (mptt) cc_final: 0.8284 (mmtt) REVERT: C 1158 MET cc_start: 0.8848 (mmp) cc_final: 0.8547 (mmp) REVERT: C 1325 LEU cc_start: 0.7571 (mm) cc_final: 0.7284 (mm) REVERT: C 1385 TRP cc_start: 0.6551 (m100) cc_final: 0.5301 (m100) REVERT: D 215 MET cc_start: 0.6443 (ptp) cc_final: 0.6085 (ptp) REVERT: D 665 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 680 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8268 (tm-30) REVERT: D 743 TRP cc_start: 0.7232 (OUTLIER) cc_final: 0.6500 (t60) REVERT: D 760 MET cc_start: 0.8819 (tmm) cc_final: 0.8572 (ptm) REVERT: D 844 MET cc_start: 0.9057 (mtm) cc_final: 0.8408 (ptp) REVERT: D 918 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7773 (mmtt) REVERT: D 923 LYS cc_start: 0.9288 (tppt) cc_final: 0.8804 (ptmt) REVERT: D 1125 GLU cc_start: 0.8655 (tt0) cc_final: 0.8452 (tt0) REVERT: D 1158 MET cc_start: 0.9025 (mmm) cc_final: 0.8762 (mmt) outliers start: 86 outliers final: 42 residues processed: 498 average time/residue: 0.2435 time to fit residues: 203.3306 Evaluate side-chains 421 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 372 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 435 GLN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1072 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 287 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 444 GLN 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 803 ILE Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 925 ILE 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 337 LEU Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 749 VAL Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 925 ILE Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1149 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 419 PHE Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 803 ILE 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 479 optimal weight: 0.9990 chunk 136 optimal weight: 50.0000 chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 50.0000 chunk 274 optimal weight: 3.9990 chunk 249 optimal weight: 30.0000 chunk 334 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 451 optimal weight: 0.3980 chunk 61 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 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** B 168 ASN B 346 ASN B 380 GLN ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1346 HIS C 380 GLN C 444 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 GLN D 451 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.190413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.129282 restraints weight = 89995.118| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 5.50 r_work: 0.3633 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 41920 Z= 0.124 Angle : 0.643 14.574 57244 Z= 0.324 Chirality : 0.042 0.214 6580 Planarity : 0.005 0.061 7264 Dihedral : 7.595 64.543 6166 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.90 % Favored : 90.95 % Rotamer: Outliers : 2.29 % Allowed : 15.34 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.11), residues: 5368 helix: 0.17 (0.11), residues: 2452 sheet: -0.36 (0.27), residues: 372 loop : -2.62 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 464 TYR 0.027 0.001 TYR B 833 PHE 0.021 0.001 PHE C 937 TRP 0.025 0.001 TRP D 743 HIS 0.016 0.001 HIS C 559 Details of bonding type rmsd covalent geometry : bond 0.00274 (41920) covalent geometry : angle 0.64257 (57244) hydrogen bonds : bond 0.03901 ( 1710) hydrogen bonds : angle 4.60224 ( 4926) *********************** 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 493 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 403 time to evaluate : 1.528 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: A 215 MET cc_start: 0.6207 (ptp) cc_final: 0.5834 (ptp) REVERT: A 404 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6238 (mmtp) REVERT: A 505 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: A 680 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8225 (tm-30) REVERT: A 692 GLU cc_start: 0.9256 (tp30) cc_final: 0.8970 (tp30) REVERT: A 728 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8823 (mtmt) REVERT: A 743 TRP cc_start: 0.7628 (OUTLIER) cc_final: 0.6587 (t60) REVERT: A 844 MET cc_start: 0.8479 (mtm) cc_final: 0.7474 (tmm) REVERT: A 868 TRP cc_start: 0.6278 (m100) cc_final: 0.5712 (m100) REVERT: A 912 HIS cc_start: 0.8262 (t70) cc_final: 0.7848 (t70) REVERT: A 918 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7669 (mmtt) REVERT: A 930 MET cc_start: 0.3968 (tpt) cc_final: 0.3741 (tpt) REVERT: A 1125 GLU cc_start: 0.8836 (tt0) cc_final: 0.8594 (tt0) REVERT: A 1371 MET cc_start: 0.5719 (mmp) cc_final: 0.5458 (mmm) REVERT: B 122 MET cc_start: 0.8876 (mpp) cc_final: 0.8267 (mpp) REVERT: B 196 LYS cc_start: 0.8743 (tttt) cc_final: 0.8484 (tttt) REVERT: B 199 GLN cc_start: 0.8284 (pp30) cc_final: 0.8013 (pp30) REVERT: B 215 MET cc_start: 0.7323 (ptp) cc_final: 0.7065 (ptp) REVERT: B 426 GLN cc_start: 0.5473 (OUTLIER) cc_final: 0.3205 (pm20) REVERT: B 463 ASN cc_start: 0.9203 (t0) cc_final: 0.8762 (t0) REVERT: B 557 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: B 844 MET cc_start: 0.8674 (mtm) cc_final: 0.7690 (tmm) REVERT: B 857 MET cc_start: 0.5459 (tpt) cc_final: 0.5195 (tpt) REVERT: B 868 TRP cc_start: 0.6265 (m100) cc_final: 0.6054 (m100) REVERT: B 930 MET cc_start: 0.2834 (tpt) cc_final: 0.2578 (tpt) REVERT: B 948 PHE cc_start: 0.3885 (m-80) cc_final: 0.3452 (t80) REVERT: B 965 TRP cc_start: 0.4668 (m100) cc_final: 0.4376 (m100) REVERT: B 1145 GLU cc_start: 0.8875 (mp0) cc_final: 0.8258 (mp0) REVERT: B 1149 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: B 1491 LEU cc_start: 0.8548 (mp) cc_final: 0.8128 (tp) REVERT: C 122 MET cc_start: 0.8147 (mpp) cc_final: 0.7372 (mpp) REVERT: C 215 MET cc_start: 0.7348 (mpp) cc_final: 0.6970 (mtt) REVERT: C 292 HIS cc_start: 0.7199 (t70) cc_final: 0.6896 (t70) REVERT: C 444 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7246 (pp30) REVERT: C 558 MET cc_start: 0.8814 (mmm) cc_final: 0.8153 (mmt) REVERT: C 571 ASP cc_start: 0.7614 (m-30) cc_final: 0.7124 (p0) REVERT: C 692 GLU cc_start: 0.9289 (tp30) cc_final: 0.8936 (tp30) REVERT: C 699 GLU cc_start: 0.8334 (tp30) cc_final: 0.8123 (tp30) REVERT: C 778 LEU cc_start: 0.8274 (mt) cc_final: 0.7689 (tp) REVERT: C 835 TRP cc_start: 0.3869 (t-100) cc_final: 0.2999 (t-100) REVERT: C 844 MET cc_start: 0.9135 (mtm) cc_final: 0.8654 (ptp) REVERT: C 911 MET cc_start: 0.7943 (mmp) cc_final: 0.7587 (mmm) REVERT: C 918 LYS cc_start: 0.8741 (mptt) cc_final: 0.8334 (mmtt) REVERT: C 1125 GLU cc_start: 0.8652 (tt0) cc_final: 0.8252 (tt0) REVERT: C 1145 GLU cc_start: 0.8496 (mp0) cc_final: 0.8036 (mp0) REVERT: C 1149 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: C 1325 LEU cc_start: 0.7294 (mm) cc_final: 0.7057 (mm) REVERT: C 1385 TRP cc_start: 0.6648 (m100) cc_final: 0.5464 (m100) REVERT: D 215 MET cc_start: 0.6539 (ptp) cc_final: 0.6094 (ptp) REVERT: D 435 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.9072 (pm20) REVERT: D 501 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8178 (mtpp) REVERT: D 505 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8700 (mp0) REVERT: D 680 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8283 (tm-30) REVERT: D 726 ASP cc_start: 0.7778 (m-30) cc_final: 0.7140 (m-30) REVERT: D 770 LEU cc_start: 0.8060 (tt) cc_final: 0.7751 (pt) REVERT: D 844 MET cc_start: 0.9043 (mtm) cc_final: 0.8365 (ptp) REVERT: D 911 MET cc_start: 0.8659 (mmm) cc_final: 0.8355 (mmm) REVERT: D 918 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7775 (mmtt) REVERT: D 923 LYS cc_start: 0.9306 (tppt) cc_final: 0.9037 (mttt) REVERT: D 1116 ASN cc_start: 0.8151 (t0) cc_final: 0.7950 (t0) REVERT: D 1125 GLU cc_start: 0.8776 (tt0) cc_final: 0.8522 (tt0) REVERT: D 1145 GLU cc_start: 0.8523 (tp30) cc_final: 0.8153 (tp30) REVERT: D 1149 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8203 (mp0) outliers start: 90 outliers final: 49 residues processed: 478 average time/residue: 0.2371 time to fit residues: 192.0946 Evaluate side-chains 435 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 435 GLN Chi-restraints excluded: chain A residue 460 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 687 ILE 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 929 ARG Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1072 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 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 557 GLN 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 840 VAL 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 337 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 444 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 749 VAL 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 C residue 1149 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 353 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 730 VAL Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 857 MET Chi-restraints excluded: chain D residue 940 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 38 optimal weight: 0.8980 chunk 516 optimal weight: 30.0000 chunk 321 optimal weight: 10.0000 chunk 393 optimal weight: 20.0000 chunk 434 optimal weight: 10.0000 chunk 316 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 184 optimal weight: 0.4980 chunk 365 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 overall best weight: 1.7782 ------------------------------------------------------------------------------- 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 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** 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 451 ASN ** D 495 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.188734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.126807 restraints weight = 89719.857| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 5.23 r_work: 0.3600 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4008 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= 0.142 Angle : 0.645 17.410 57244 Z= 0.326 Chirality : 0.042 0.199 6580 Planarity : 0.005 0.070 7264 Dihedral : 7.132 62.240 6164 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.74 % Favored : 91.11 % Rotamer: Outliers : 2.85 % Allowed : 16.00 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.11), residues: 5368 helix: 0.36 (0.11), residues: 2440 sheet: -0.27 (0.26), residues: 372 loop : -2.53 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 411 TYR 0.024 0.001 TYR B 833 PHE 0.015 0.001 PHE D 617 TRP 0.023 0.001 TRP D 944 HIS 0.009 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00329 (41920) covalent geometry : angle 0.64530 (57244) hydrogen bonds : bond 0.03937 ( 1710) hydrogen bonds : angle 4.54543 ( 4926) *********************** 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 504 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 392 time to evaluate : 1.538 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: 0.6325 (ptp) cc_final: 0.5901 (ptp) REVERT: A 404 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6377 (mmtp) REVERT: A 426 GLN cc_start: 0.4617 (OUTLIER) cc_final: 0.2073 (pm20) REVERT: A 463 ASN cc_start: 0.9224 (t0) cc_final: 0.9021 (t0) REVERT: A 505 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: A 557 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 680 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8278 (tm-30) REVERT: A 692 GLU cc_start: 0.9302 (tp30) cc_final: 0.8955 (tp30) REVERT: A 728 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8778 (mtmt) REVERT: A 743 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.6641 (t60) REVERT: A 844 MET cc_start: 0.8518 (mtm) cc_final: 0.7461 (tmm) REVERT: A 918 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7732 (mmtt) REVERT: A 1371 MET cc_start: 0.5766 (mmp) cc_final: 0.5121 (mmm) REVERT: B 122 MET cc_start: 0.8864 (mpp) cc_final: 0.8219 (mpp) REVERT: B 196 LYS cc_start: 0.8711 (tttt) cc_final: 0.8426 (ttpt) REVERT: B 199 GLN cc_start: 0.8300 (pp30) cc_final: 0.8035 (pp30) REVERT: B 215 MET cc_start: 0.7390 (ptp) cc_final: 0.6848 (ptp) REVERT: B 295 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.5902 (m-10) REVERT: B 426 GLN cc_start: 0.5419 (OUTLIER) cc_final: 0.3283 (pm20) REVERT: B 463 ASN cc_start: 0.9233 (t0) cc_final: 0.8773 (t0) REVERT: B 557 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: B 726 ASP cc_start: 0.7243 (m-30) cc_final: 0.7010 (m-30) REVERT: B 844 MET cc_start: 0.8702 (mtm) cc_final: 0.7701 (tmm) REVERT: B 857 MET cc_start: 0.5597 (tpt) cc_final: 0.5340 (tpt) REVERT: B 868 TRP cc_start: 0.6310 (m100) cc_final: 0.6096 (m100) REVERT: B 930 MET cc_start: 0.2547 (tpt) cc_final: 0.2334 (tpt) REVERT: B 948 PHE cc_start: 0.3844 (m-80) cc_final: 0.3536 (t80) REVERT: B 1137 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8804 (tm-30) REVERT: B 1145 GLU cc_start: 0.8835 (mp0) cc_final: 0.8195 (mp0) REVERT: B 1149 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 1491 LEU cc_start: 0.8625 (mp) cc_final: 0.8248 (tp) REVERT: C 122 MET cc_start: 0.8142 (mpp) cc_final: 0.7341 (mpp) REVERT: C 215 MET cc_start: 0.7428 (mpp) cc_final: 0.7049 (mtt) REVERT: C 292 HIS cc_start: 0.7268 (t70) cc_final: 0.6990 (t70) REVERT: C 426 GLN cc_start: 0.4341 (OUTLIER) cc_final: 0.3468 (mm-40) REVERT: C 557 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: C 558 MET cc_start: 0.8838 (mmm) cc_final: 0.8274 (mmt) REVERT: C 571 ASP cc_start: 0.7578 (m-30) cc_final: 0.7060 (p0) REVERT: C 669 THR cc_start: 0.6960 (t) cc_final: 0.6597 (t) REVERT: C 692 GLU cc_start: 0.9335 (tp30) cc_final: 0.8981 (tp30) REVERT: C 778 LEU cc_start: 0.8266 (mt) cc_final: 0.7682 (tp) REVERT: C 844 MET cc_start: 0.9081 (mtm) cc_final: 0.8581 (ptp) REVERT: C 911 MET cc_start: 0.7973 (mmp) cc_final: 0.7634 (mmm) REVERT: C 918 LYS cc_start: 0.8769 (mptt) cc_final: 0.8368 (mmtt) REVERT: C 965 TRP cc_start: 0.4812 (m100) cc_final: 0.4469 (m100) REVERT: C 1125 GLU cc_start: 0.8670 (tt0) cc_final: 0.8255 (tt0) REVERT: C 1145 GLU cc_start: 0.8507 (mp0) cc_final: 0.7962 (mp0) REVERT: C 1149 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: C 1325 LEU cc_start: 0.7227 (mm) cc_final: 0.6987 (mm) REVERT: C 1385 TRP cc_start: 0.6732 (m100) cc_final: 0.5461 (m100) REVERT: D 215 MET cc_start: 0.6385 (ptp) cc_final: 0.6028 (ptp) REVERT: D 501 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8282 (mtpp) REVERT: D 505 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: D 623 ARG cc_start: 0.7578 (mpt180) cc_final: 0.7356 (mpt180) REVERT: D 680 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8276 (tm-30) REVERT: D 726 ASP cc_start: 0.7799 (m-30) cc_final: 0.7102 (m-30) REVERT: D 743 TRP cc_start: 0.7430 (OUTLIER) cc_final: 0.6737 (t60) REVERT: D 760 MET cc_start: 0.8818 (tmm) cc_final: 0.8583 (ptm) REVERT: D 844 MET cc_start: 0.9053 (mtm) cc_final: 0.8357 (ptp) REVERT: D 918 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7832 (mmtt) REVERT: D 923 LYS cc_start: 0.9313 (tppt) cc_final: 0.8876 (ptmt) REVERT: D 1116 ASN cc_start: 0.8330 (t0) cc_final: 0.8083 (t0) REVERT: D 1145 GLU cc_start: 0.8617 (tp30) cc_final: 0.8099 (tp30) REVERT: D 1149 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8125 (mp0) outliers start: 112 outliers final: 70 residues processed: 489 average time/residue: 0.2372 time to fit residues: 198.1907 Evaluate side-chains 460 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 376 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU 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 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 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 929 ARG Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1072 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 295 TYR 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 505 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 557 GLN 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 803 ILE 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 929 ARG 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 190 PHE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 276 CYS 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 520 LEU Chi-restraints excluded: chain C residue 557 GLN Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 VAL 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 1149 GLU Chi-restraints excluded: chain C residue 1477 VAL 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 460 VAL Chi-restraints excluded: chain D residue 505 GLU 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 704 LEU 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 857 MET Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 0.3980 chunk 169 optimal weight: 0.7980 chunk 474 optimal weight: 0.5980 chunk 240 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 461 optimal weight: 2.9990 chunk 503 optimal weight: 20.0000 chunk 484 optimal weight: 3.9990 chunk 251 optimal weight: 30.0000 chunk 358 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 495 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.189697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.129573 restraints weight = 90013.169| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 5.54 r_work: 0.3623 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41920 Z= 0.118 Angle : 0.633 13.960 57244 Z= 0.318 Chirality : 0.042 0.189 6580 Planarity : 0.004 0.058 7264 Dihedral : 6.805 58.456 6164 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 2.57 % Allowed : 17.07 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.11), residues: 5368 helix: 0.55 (0.11), residues: 2448 sheet: -0.16 (0.26), residues: 372 loop : -2.47 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 555 TYR 0.023 0.001 TYR B 833 PHE 0.016 0.001 PHE D 936 TRP 0.034 0.001 TRP A 944 HIS 0.008 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00261 (41920) covalent geometry : angle 0.63323 (57244) hydrogen bonds : bond 0.03592 ( 1710) hydrogen bonds : angle 4.40638 ( 4926) *********************** 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 499 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 398 time to evaluate : 1.644 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: 0.6514 (ptp) cc_final: 0.6048 (ptp) REVERT: A 404 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6413 (mmtp) REVERT: A 426 GLN cc_start: 0.4476 (OUTLIER) cc_final: 0.2058 (pm20) REVERT: A 463 ASN cc_start: 0.9205 (t0) cc_final: 0.8864 (t0) REVERT: A 557 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7506 (tt0) REVERT: A 680 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8299 (tm-30) REVERT: A 728 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8717 (mtmt) REVERT: A 743 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.6553 (t60) REVERT: A 760 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7933 (ptm) REVERT: A 844 MET cc_start: 0.8513 (mtm) cc_final: 0.7478 (tmt) REVERT: A 918 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7714 (mmtt) REVERT: A 1371 MET cc_start: 0.5887 (mmp) cc_final: 0.4972 (mmm) REVERT: B 122 MET cc_start: 0.8919 (mpp) cc_final: 0.8406 (mpp) REVERT: B 215 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6819 (ptp) REVERT: B 426 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.3194 (pm20) REVERT: B 463 ASN cc_start: 0.9256 (t0) cc_final: 0.8784 (t0) REVERT: B 557 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: B 697 ASP cc_start: 0.8562 (t0) cc_final: 0.7697 (t0) REVERT: B 726 ASP cc_start: 0.7215 (m-30) cc_final: 0.6944 (m-30) REVERT: B 844 MET cc_start: 0.8706 (mtm) cc_final: 0.7711 (tmm) REVERT: B 857 MET cc_start: 0.5567 (tpt) cc_final: 0.5316 (tpt) REVERT: B 1137 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8760 (tm-30) REVERT: B 1491 LEU cc_start: 0.8573 (mp) cc_final: 0.8164 (tp) REVERT: C 122 MET cc_start: 0.8168 (mpp) cc_final: 0.7354 (mpp) REVERT: C 215 MET cc_start: 0.7468 (mpp) cc_final: 0.7048 (mtt) REVERT: C 292 HIS cc_start: 0.7238 (t70) cc_final: 0.6950 (t70) REVERT: C 426 GLN cc_start: 0.4542 (OUTLIER) cc_final: 0.3749 (mm-40) REVERT: C 483 ASP cc_start: 0.8484 (t0) cc_final: 0.8097 (m-30) REVERT: C 505 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8682 (mp0) REVERT: C 557 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: C 558 MET cc_start: 0.8856 (mmm) cc_final: 0.8245 (mmt) REVERT: C 692 GLU cc_start: 0.9325 (tp30) cc_final: 0.8977 (tp30) REVERT: C 699 GLU cc_start: 0.8257 (tp30) cc_final: 0.8056 (tp30) REVERT: C 778 LEU cc_start: 0.8228 (mt) cc_final: 0.7703 (tp) REVERT: C 844 MET cc_start: 0.9086 (mtm) cc_final: 0.8575 (ptp) REVERT: C 918 LYS cc_start: 0.8778 (mptt) cc_final: 0.8341 (mmtt) REVERT: C 1122 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8111 (mt) REVERT: C 1125 GLU cc_start: 0.8680 (tt0) cc_final: 0.8227 (tt0) REVERT: C 1325 LEU cc_start: 0.7004 (mm) cc_final: 0.6783 (mm) REVERT: C 1385 TRP cc_start: 0.6840 (m100) cc_final: 0.5514 (m100) REVERT: D 215 MET cc_start: 0.6485 (ptp) cc_final: 0.6105 (ptp) REVERT: D 501 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8173 (mtpp) REVERT: D 505 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8667 (mp0) REVERT: D 680 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8268 (tm-30) REVERT: D 726 ASP cc_start: 0.7686 (m-30) cc_final: 0.6921 (m-30) REVERT: D 743 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.6697 (t60) REVERT: D 844 MET cc_start: 0.9023 (mtm) cc_final: 0.8290 (ptp) REVERT: D 916 ILE cc_start: 0.8119 (tp) cc_final: 0.7786 (tp) REVERT: D 918 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7782 (mmtt) REVERT: D 923 LYS cc_start: 0.9295 (tppt) cc_final: 0.8914 (ptmt) REVERT: D 1156 ASP cc_start: 0.9373 (t0) cc_final: 0.9138 (t0) REVERT: D 1489 LYS cc_start: 0.9410 (mtpt) cc_final: 0.9089 (mmmt) outliers start: 101 outliers final: 67 residues processed: 479 average time/residue: 0.2325 time to fit residues: 191.4022 Evaluate side-chains 454 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 373 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 426 GLN Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 460 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 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 817 LEU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 962 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 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 505 GLU Chi-restraints excluded: chain B residue 557 GLN 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 836 LEU Chi-restraints excluded: chain B residue 927 VAL 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 557 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 704 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 1118 GLU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain C residue 1149 GLU Chi-restraints excluded: chain C residue 1477 VAL 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 353 VAL Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 505 GLU 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 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 857 MET Chi-restraints excluded: chain D residue 934 VAL Chi-restraints excluded: chain D residue 1151 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 244 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 134 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 476 optimal weight: 1.9990 chunk 515 optimal weight: 9.9990 chunk 139 optimal weight: 0.0770 chunk 162 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 overall best weight: 4.2146 ------------------------------------------------------------------------------- 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** A1058 HIS A1450 GLN ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1450 GLN C 156 HIS C 168 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS C1437 ASN D 156 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 426 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 HIS ** D 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1058 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.184292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.117582 restraints weight = 89461.488| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.97 r_work: 0.3551 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 41920 Z= 0.249 Angle : 0.741 12.585 57244 Z= 0.377 Chirality : 0.045 0.221 6580 Planarity : 0.005 0.058 7264 Dihedral : 6.945 57.862 6164 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.58 % Favored : 90.28 % Rotamer: Outliers : 3.80 % Allowed : 16.97 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.11), residues: 5368 helix: 0.34 (0.10), residues: 2480 sheet: -0.43 (0.25), residues: 404 loop : -2.52 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1356 TYR 0.029 0.002 TYR A 682 PHE 0.021 0.002 PHE A 513 TRP 0.032 0.002 TRP B 944 HIS 0.017 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00578 (41920) covalent geometry : angle 0.74080 (57244) hydrogen bonds : bond 0.04807 ( 1710) hydrogen bonds : angle 4.74074 ( 4926) *********************** 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 553 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 404 time to evaluate : 1.827 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: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.6742 (ptp) cc_final: 0.6342 (ptp) REVERT: A 420 ARG cc_start: 0.4685 (OUTLIER) cc_final: 0.2630 (tpp-160) REVERT: A 426 GLN cc_start: 0.4507 (OUTLIER) cc_final: 0.2048 (pm20) REVERT: A 463 ASN cc_start: 0.9316 (t0) cc_final: 0.9047 (t0) REVERT: A 571 ASP cc_start: 0.7275 (m-30) cc_final: 0.6815 (p0) REVERT: A 623 ARG cc_start: 0.7625 (mpp-170) cc_final: 0.7312 (mpt180) REVERT: A 728 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8811 (mtmt) REVERT: A 743 TRP cc_start: 0.7959 (OUTLIER) cc_final: 0.6992 (t60) REVERT: A 844 MET cc_start: 0.8579 (mtm) cc_final: 0.7589 (tmt) REVERT: A 916 ILE cc_start: 0.8014 (tp) cc_final: 0.7743 (tp) REVERT: A 918 LYS cc_start: 0.8676 (mtmt) cc_final: 0.8131 (mmtt) REVERT: A 1149 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8230 (mp0) REVERT: A 1158 MET cc_start: 0.8212 (mmt) cc_final: 0.7821 (mmp) REVERT: B 122 MET cc_start: 0.8876 (mpp) cc_final: 0.8546 (mpp) REVERT: B 196 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8569 (ttpp) REVERT: B 415 LEU cc_start: 0.7701 (mm) cc_final: 0.7487 (mm) REVERT: B 417 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8531 (p) REVERT: B 426 GLN cc_start: 0.5011 (OUTLIER) cc_final: 0.3063 (pm20) REVERT: B 463 ASN cc_start: 0.9396 (t0) cc_final: 0.9059 (t0) REVERT: B 557 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: B 726 ASP cc_start: 0.7570 (m-30) cc_final: 0.6925 (m-30) REVERT: B 743 TRP cc_start: 0.7975 (OUTLIER) cc_final: 0.7021 (t60) REVERT: B 844 MET cc_start: 0.8735 (mtm) cc_final: 0.7744 (tmm) REVERT: B 857 MET cc_start: 0.5615 (tpt) cc_final: 0.5380 (tpt) REVERT: B 948 PHE cc_start: 0.6035 (OUTLIER) cc_final: 0.5626 (t80) REVERT: B 1137 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8733 (tm-30) REVERT: C 122 MET cc_start: 0.8351 (mpp) cc_final: 0.7674 (mpp) REVERT: C 168 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7005 (t0) REVERT: C 215 MET cc_start: 0.7576 (mpp) cc_final: 0.7167 (mtt) REVERT: C 292 HIS cc_start: 0.7506 (t70) cc_final: 0.7242 (t70) REVERT: C 426 GLN cc_start: 0.4428 (OUTLIER) cc_final: 0.3628 (mm110) REVERT: C 480 LYS cc_start: 0.8127 (tppt) cc_final: 0.7819 (pttt) REVERT: C 483 ASP cc_start: 0.8433 (t0) cc_final: 0.8141 (m-30) REVERT: C 505 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8621 (mp0) REVERT: C 557 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: C 623 ARG cc_start: 0.7567 (mpp-170) cc_final: 0.7242 (mpt180) REVERT: C 692 GLU cc_start: 0.9341 (tp30) cc_final: 0.9120 (tp30) REVERT: C 699 GLU cc_start: 0.8426 (tp30) cc_final: 0.8223 (tp30) REVERT: C 743 TRP cc_start: 0.7917 (OUTLIER) cc_final: 0.6871 (t60) REVERT: C 744 TRP cc_start: 0.8846 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: C 844 MET cc_start: 0.9154 (mtm) cc_final: 0.8688 (ptp) REVERT: C 911 MET cc_start: 0.7896 (mmm) cc_final: 0.7583 (mmp) REVERT: C 918 LYS cc_start: 0.8815 (mptt) cc_final: 0.8369 (mmtt) REVERT: C 965 TRP cc_start: 0.4838 (m100) cc_final: 0.4472 (m100) REVERT: D 215 MET cc_start: 0.6578 (ptp) cc_final: 0.6188 (ptp) REVERT: D 501 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8400 (mtpp) REVERT: D 505 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8633 (mp0) REVERT: D 571 ASP cc_start: 0.7397 (m-30) cc_final: 0.6941 (p0) REVERT: D 680 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8418 (tm-30) REVERT: D 743 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.6974 (t60) REVERT: D 844 MET cc_start: 0.9055 (mtm) cc_final: 0.8318 (ptp) REVERT: D 918 LYS cc_start: 0.8442 (mtmt) cc_final: 0.7991 (mmtt) REVERT: D 1149 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8527 (mp0) REVERT: D 1156 ASP cc_start: 0.9408 (t0) cc_final: 0.9181 (t0) outliers start: 149 outliers final: 104 residues processed: 532 average time/residue: 0.2448 time to fit residues: 219.3403 Evaluate side-chains 494 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 374 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 505 GLU 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 903 PHE Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 962 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 1477 VAL Chi-restraints excluded: chain B residue 195 VAL 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 351 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 557 GLN 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 836 LEU Chi-restraints excluded: chain B residue 840 VAL Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 948 PHE 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 168 ASN 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 467 ILE Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 557 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 704 LEU 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 749 VAL 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 1149 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 419 PHE Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 505 GLU 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 770 LEU Chi-restraints excluded: chain D residue 803 ILE Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 903 PHE Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 934 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 45 optimal weight: 0.8980 chunk 401 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 chunk 528 optimal weight: 40.0000 chunk 54 optimal weight: 30.0000 chunk 224 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 332 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** B 346 ASN B 953 GLN C 168 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 953 GLN D1056 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.187601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.124683 restraints weight = 89121.991| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 4.92 r_work: 0.3602 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.5015 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= 0.126 Angle : 0.660 13.533 57244 Z= 0.332 Chirality : 0.042 0.218 6580 Planarity : 0.004 0.056 7264 Dihedral : 6.763 56.007 6162 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.76 % Favored : 91.15 % Rotamer: Outliers : 2.83 % Allowed : 18.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.11), residues: 5368 helix: 0.66 (0.11), residues: 2456 sheet: -0.32 (0.25), residues: 396 loop : -2.45 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 464 TYR 0.019 0.001 TYR B 833 PHE 0.021 0.001 PHE D 936 TRP 0.040 0.001 TRP A1385 HIS 0.013 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00284 (41920) covalent geometry : angle 0.66003 (57244) hydrogen bonds : bond 0.03711 ( 1710) hydrogen bonds : angle 4.45524 ( 4926) *********************** 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 509 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 398 time to evaluate : 1.639 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: symmetry clash REVERT: A 215 MET cc_start: 0.6660 (ptp) cc_final: 0.6232 (ptp) REVERT: A 404 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6731 (mmtp) REVERT: A 463 ASN cc_start: 0.9309 (t0) cc_final: 0.9002 (t0) REVERT: A 557 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: A 728 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8706 (mtmt) REVERT: A 743 TRP cc_start: 0.7817 (OUTLIER) cc_final: 0.6934 (t60) REVERT: A 844 MET cc_start: 0.8555 (mtm) cc_final: 0.7555 (tmt) REVERT: A 1158 MET cc_start: 0.8291 (mmt) cc_final: 0.7909 (mmp) REVERT: B 122 MET cc_start: 0.8888 (mpp) cc_final: 0.8180 (mpp) REVERT: B 215 MET cc_start: 0.7171 (ptp) cc_final: 0.6955 (ptp) REVERT: B 415 LEU cc_start: 0.7590 (mm) cc_final: 0.7332 (mm) REVERT: B 426 GLN cc_start: 0.5015 (OUTLIER) cc_final: 0.3105 (pm20) REVERT: B 435 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8925 (pm20) REVERT: B 463 ASN cc_start: 0.9421 (t0) cc_final: 0.9063 (t0) REVERT: B 557 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: B 697 ASP cc_start: 0.8625 (t0) cc_final: 0.7749 (t0) REVERT: B 728 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8681 (mtmt) REVERT: B 743 TRP cc_start: 0.7923 (OUTLIER) cc_final: 0.7006 (t60) REVERT: B 844 MET cc_start: 0.8716 (mtm) cc_final: 0.7709 (tmm) REVERT: B 857 MET cc_start: 0.5510 (tpt) cc_final: 0.5298 (tpt) REVERT: B 1117 GLU cc_start: 0.8394 (tp30) cc_final: 0.8116 (tp30) REVERT: B 1137 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8704 (tm-30) REVERT: B 1491 LEU cc_start: 0.8716 (mp) cc_final: 0.8350 (tp) REVERT: C 122 MET cc_start: 0.8326 (mpp) cc_final: 0.7586 (mpp) REVERT: C 168 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.6904 (t0) REVERT: C 215 MET cc_start: 0.7594 (mpp) cc_final: 0.7147 (mtt) REVERT: C 292 HIS cc_start: 0.7423 (t70) cc_final: 0.7165 (t70) REVERT: C 426 GLN cc_start: 0.4458 (OUTLIER) cc_final: 0.3696 (mm110) REVERT: C 480 LYS cc_start: 0.7803 (tppt) cc_final: 0.7471 (pttt) REVERT: C 505 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8590 (mp0) REVERT: C 557 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: C 692 GLU cc_start: 0.9287 (tp30) cc_final: 0.8932 (tp30) REVERT: C 699 GLU cc_start: 0.8204 (tp30) cc_final: 0.7907 (tp30) REVERT: C 744 TRP cc_start: 0.8791 (OUTLIER) cc_final: 0.8472 (m-10) REVERT: C 778 LEU cc_start: 0.8185 (mt) cc_final: 0.7573 (tp) REVERT: C 844 MET cc_start: 0.9120 (mtm) cc_final: 0.8641 (ptp) REVERT: C 911 MET cc_start: 0.7850 (mmm) cc_final: 0.7618 (mmp) REVERT: C 918 LYS cc_start: 0.8836 (mptt) cc_final: 0.8370 (mmtt) REVERT: D 215 MET cc_start: 0.6595 (ptp) cc_final: 0.6167 (ptp) REVERT: D 483 ASP cc_start: 0.8835 (t0) cc_final: 0.8464 (t0) REVERT: D 501 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8226 (mtpp) REVERT: D 505 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8613 (mp0) REVERT: D 557 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: D 680 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8352 (tm-30) REVERT: D 723 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: D 726 ASP cc_start: 0.7217 (m-30) cc_final: 0.6496 (m-30) REVERT: D 743 TRP cc_start: 0.7587 (OUTLIER) cc_final: 0.7009 (t60) REVERT: D 844 MET cc_start: 0.9007 (mtm) cc_final: 0.8243 (ptp) REVERT: D 916 ILE cc_start: 0.8223 (tp) cc_final: 0.7907 (tp) REVERT: D 918 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7889 (mmtt) REVERT: D 1149 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8467 (mp0) outliers start: 111 outliers final: 79 residues processed: 493 average time/residue: 0.2377 time to fit residues: 198.5572 Evaluate side-chains 469 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 374 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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 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 803 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 962 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 237 ILE 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 351 VAL Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 648 CYS 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 836 LEU Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1325 LEU Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 237 ILE 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 557 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 744 TRP Chi-restraints excluded: chain C residue 749 VAL 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 1149 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 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 419 PHE Chi-restraints excluded: chain D residue 435 GLN Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 557 GLN 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 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 905 LEU Chi-restraints excluded: chain D residue 934 VAL Chi-restraints excluded: chain D residue 1072 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 181 optimal weight: 0.4980 chunk 162 optimal weight: 20.0000 chunk 437 optimal weight: 9.9990 chunk 193 optimal weight: 0.5980 chunk 413 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 173 optimal weight: 5.9990 chunk 54 optimal weight: 40.0000 chunk 156 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1450 GLN D 161 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.186681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.123263 restraints weight = 89714.135| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 5.27 r_work: 0.3566 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41920 Z= 0.136 Angle : 0.669 14.657 57244 Z= 0.335 Chirality : 0.042 0.196 6580 Planarity : 0.004 0.057 7264 Dihedral : 6.659 54.760 6162 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.96 % Favored : 90.95 % Rotamer: Outliers : 2.93 % Allowed : 18.93 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.12), residues: 5368 helix: 0.74 (0.11), residues: 2464 sheet: -0.40 (0.25), residues: 412 loop : -2.41 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 555 TYR 0.019 0.001 TYR A1050 PHE 0.019 0.001 PHE D 936 TRP 0.045 0.002 TRP D1355 HIS 0.013 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00317 (41920) covalent geometry : angle 0.66918 (57244) hydrogen bonds : bond 0.03745 ( 1710) hydrogen bonds : angle 4.41816 ( 4926) *********************** 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 493 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 378 time to evaluate : 1.514 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: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.6709 (ptp) cc_final: 0.6256 (ptp) REVERT: A 404 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6734 (mmtp) REVERT: A 420 ARG cc_start: 0.4584 (OUTLIER) cc_final: 0.3792 (tpp-160) REVERT: A 426 GLN cc_start: 0.4560 (OUTLIER) cc_final: 0.2055 (pm20) REVERT: A 463 ASN cc_start: 0.9331 (t0) cc_final: 0.9048 (t0) REVERT: A 505 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: A 557 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: A 692 GLU cc_start: 0.9249 (tp30) cc_final: 0.8960 (tp30) REVERT: A 728 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8708 (mtmt) REVERT: A 743 TRP cc_start: 0.7755 (OUTLIER) cc_final: 0.6906 (t60) REVERT: A 844 MET cc_start: 0.8558 (mtm) cc_final: 0.7560 (tmt) REVERT: A 1149 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8362 (mp0) REVERT: A 1158 MET cc_start: 0.8178 (mmt) cc_final: 0.7955 (mmp) REVERT: B 122 MET cc_start: 0.8890 (mpp) cc_final: 0.8190 (mpp) REVERT: B 215 MET cc_start: 0.7144 (ptp) cc_final: 0.6908 (ptp) REVERT: B 426 GLN cc_start: 0.5011 (OUTLIER) cc_final: 0.3061 (pm20) REVERT: B 463 ASN cc_start: 0.9434 (t0) cc_final: 0.9099 (t0) REVERT: B 557 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: B 636 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8617 (mm-30) REVERT: B 726 ASP cc_start: 0.7404 (m-30) cc_final: 0.7143 (m-30) REVERT: B 743 TRP cc_start: 0.7916 (OUTLIER) cc_final: 0.7021 (t60) REVERT: B 844 MET cc_start: 0.8705 (mtm) cc_final: 0.7706 (tmm) REVERT: B 857 MET cc_start: 0.5557 (tpt) cc_final: 0.5348 (tpt) REVERT: B 1117 GLU cc_start: 0.8395 (tp30) cc_final: 0.8113 (tp30) REVERT: B 1137 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8670 (tm-30) REVERT: B 1491 LEU cc_start: 0.8705 (mp) cc_final: 0.8378 (tp) REVERT: C 122 MET cc_start: 0.8340 (mpp) cc_final: 0.7596 (mpp) REVERT: C 215 MET cc_start: 0.7605 (mpp) cc_final: 0.7142 (mtt) REVERT: C 292 HIS cc_start: 0.7502 (t70) cc_final: 0.7229 (t70) REVERT: C 426 GLN cc_start: 0.4569 (OUTLIER) cc_final: 0.3821 (mm110) REVERT: C 505 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: C 557 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: C 692 GLU cc_start: 0.9327 (tp30) cc_final: 0.8988 (tp30) REVERT: C 726 ASP cc_start: 0.7480 (m-30) cc_final: 0.6629 (m-30) REVERT: C 743 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.6922 (t60) REVERT: C 744 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.8523 (m-10) REVERT: C 778 LEU cc_start: 0.8176 (mt) cc_final: 0.7544 (tp) REVERT: C 844 MET cc_start: 0.9122 (mtm) cc_final: 0.8634 (ptp) REVERT: C 911 MET cc_start: 0.7896 (mmm) cc_final: 0.7664 (mmp) REVERT: C 918 LYS cc_start: 0.8854 (mptt) cc_final: 0.8414 (mmtt) REVERT: D 215 MET cc_start: 0.6651 (ptp) cc_final: 0.6206 (ptp) REVERT: D 483 ASP cc_start: 0.8829 (t0) cc_final: 0.8524 (t0) REVERT: D 501 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8216 (mtpp) REVERT: D 505 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8654 (mp0) REVERT: D 557 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: D 665 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8530 (tp30) REVERT: D 680 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8326 (tm-30) REVERT: D 743 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6997 (t60) REVERT: D 844 MET cc_start: 0.9001 (mtm) cc_final: 0.8260 (ptp) REVERT: D 916 ILE cc_start: 0.8202 (tp) cc_final: 0.7899 (tp) REVERT: D 918 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7933 (mmtt) REVERT: D 1149 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8499 (mp0) outliers start: 115 outliers final: 86 residues processed: 476 average time/residue: 0.2268 time to fit residues: 183.7571 Evaluate side-chains 478 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 375 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 803 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 962 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 237 ILE 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 351 VAL 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 442 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 648 CYS 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 836 LEU Chi-restraints excluded: chain B residue 903 PHE 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 1325 LEU 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 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 557 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 704 LEU 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 749 VAL 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 1149 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 326 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 419 PHE 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 557 GLN 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 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 905 LEU Chi-restraints excluded: chain D residue 1072 GLU Chi-restraints excluded: chain D residue 1151 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 234 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 384 optimal weight: 20.0000 chunk 277 optimal weight: 0.0570 chunk 339 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 269 optimal weight: 6.9990 chunk 438 optimal weight: 9.9990 chunk 235 optimal weight: 0.6980 overall best weight: 1.7504 ------------------------------------------------------------------------------- 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 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** A 973 HIS B 248 HIS B 271 GLN C 346 ASN ** C 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.186391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.122140 restraints weight = 88813.365| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.24 r_work: 0.3597 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41920 Z= 0.142 Angle : 0.671 11.370 57244 Z= 0.338 Chirality : 0.042 0.203 6580 Planarity : 0.004 0.057 7264 Dihedral : 6.574 55.192 6162 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.07 % Favored : 90.85 % Rotamer: Outliers : 2.62 % Allowed : 19.39 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.12), residues: 5368 helix: 0.82 (0.11), residues: 2472 sheet: -0.47 (0.24), residues: 416 loop : -2.40 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 555 TYR 0.018 0.001 TYR B 833 PHE 0.020 0.001 PHE D 936 TRP 0.056 0.002 TRP A 944 HIS 0.011 0.001 HIS B 559 Details of bonding type rmsd covalent geometry : bond 0.00331 (41920) covalent geometry : angle 0.67064 (57244) hydrogen bonds : bond 0.03746 ( 1710) hydrogen bonds : angle 4.39382 ( 4926) ********************** 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 491 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 388 time to evaluate : 1.551 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: A 215 MET cc_start: 0.6741 (ptp) cc_final: 0.6293 (ptp) REVERT: A 386 PHE cc_start: 0.8306 (m-80) cc_final: 0.7973 (m-80) REVERT: A 420 ARG cc_start: 0.4604 (OUTLIER) cc_final: 0.3580 (tpp-160) REVERT: A 426 GLN cc_start: 0.4447 (OUTLIER) cc_final: 0.1830 (pm20) REVERT: A 463 ASN cc_start: 0.9339 (t0) cc_final: 0.9085 (t0) REVERT: A 505 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 557 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: A 692 GLU cc_start: 0.9242 (tp30) cc_final: 0.8951 (tp30) REVERT: A 728 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8664 (mtmt) REVERT: A 743 TRP cc_start: 0.7707 (OUTLIER) cc_final: 0.6887 (t60) REVERT: A 844 MET cc_start: 0.8545 (mtm) cc_final: 0.7539 (tmt) REVERT: A 929 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7261 (ppt170) REVERT: A 1149 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8369 (mm-30) REVERT: B 122 MET cc_start: 0.8869 (mpp) cc_final: 0.8181 (mpp) REVERT: B 199 GLN cc_start: 0.8410 (pp30) cc_final: 0.8145 (pp30) REVERT: B 215 MET cc_start: 0.6955 (ptp) cc_final: 0.6731 (ptp) REVERT: B 426 GLN cc_start: 0.4774 (OUTLIER) cc_final: 0.2896 (pm20) REVERT: B 435 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8959 (pm20) REVERT: B 463 ASN cc_start: 0.9418 (t0) cc_final: 0.9154 (t0) REVERT: B 505 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: B 557 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 726 ASP cc_start: 0.7436 (m-30) cc_final: 0.7168 (m-30) REVERT: B 743 TRP cc_start: 0.7826 (OUTLIER) cc_final: 0.6951 (t60) REVERT: B 844 MET cc_start: 0.8741 (mtm) cc_final: 0.7738 (tmm) REVERT: B 857 MET cc_start: 0.5604 (tpt) cc_final: 0.5304 (tpt) REVERT: B 944 TRP cc_start: 0.7401 (m100) cc_final: 0.7181 (m100) REVERT: B 1117 GLU cc_start: 0.8345 (tp30) cc_final: 0.8062 (tp30) REVERT: B 1137 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8646 (tm-30) REVERT: B 1491 LEU cc_start: 0.8684 (mp) cc_final: 0.8362 (tp) REVERT: C 122 MET cc_start: 0.8372 (mpp) cc_final: 0.7664 (mpp) REVERT: C 215 MET cc_start: 0.7734 (mpp) cc_final: 0.7351 (mtt) REVERT: C 292 HIS cc_start: 0.7490 (t70) cc_final: 0.7208 (t70) REVERT: C 426 GLN cc_start: 0.4503 (OUTLIER) cc_final: 0.3792 (mm110) REVERT: C 505 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: C 557 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: C 692 GLU cc_start: 0.9296 (tp30) cc_final: 0.8944 (tp30) REVERT: C 726 ASP cc_start: 0.7556 (m-30) cc_final: 0.6682 (m-30) REVERT: C 743 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6808 (t60) REVERT: C 744 TRP cc_start: 0.8819 (OUTLIER) cc_final: 0.8517 (m-10) REVERT: C 778 LEU cc_start: 0.8129 (mt) cc_final: 0.7494 (tp) REVERT: C 844 MET cc_start: 0.9099 (mtm) cc_final: 0.8098 (tmm) REVERT: C 911 MET cc_start: 0.7950 (mmm) cc_final: 0.7648 (mmp) REVERT: C 918 LYS cc_start: 0.8860 (mptt) cc_final: 0.8395 (mmtt) REVERT: D 215 MET cc_start: 0.6484 (ptp) cc_final: 0.6035 (ptp) REVERT: D 483 ASP cc_start: 0.8822 (t0) cc_final: 0.8472 (t0) REVERT: D 501 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8163 (mtpp) REVERT: D 505 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8560 (mp0) REVERT: D 557 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: D 623 ARG cc_start: 0.7257 (mpt180) cc_final: 0.7000 (mpt180) REVERT: D 665 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8497 (tp30) REVERT: D 680 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8353 (tm-30) REVERT: D 743 TRP cc_start: 0.7543 (OUTLIER) cc_final: 0.6913 (t60) REVERT: D 844 MET cc_start: 0.9006 (mtm) cc_final: 0.8255 (ptp) REVERT: D 851 PRO cc_start: 0.5908 (Cg_endo) cc_final: 0.5605 (Cg_exo) REVERT: D 916 ILE cc_start: 0.8191 (tp) cc_final: 0.7920 (tp) REVERT: D 918 LYS cc_start: 0.8419 (mtmt) cc_final: 0.7935 (mmtt) REVERT: D 930 MET cc_start: 0.3061 (tpt) cc_final: 0.2755 (tpt) REVERT: D 1149 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8443 (mp0) outliers start: 103 outliers final: 79 residues processed: 475 average time/residue: 0.2094 time to fit residues: 169.8321 Evaluate side-chains 466 residues out of total 4748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 368 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 803 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 929 ARG Chi-restraints excluded: chain A residue 962 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 237 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 VAL 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 442 ARG Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 648 CYS 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 836 LEU 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 1443 VAL Chi-restraints excluded: chain B residue 1477 VAL 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 557 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 704 LEU 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 749 VAL Chi-restraints excluded: chain C residue 758 LEU 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 1149 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 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 460 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain D residue 557 GLN 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 730 VAL Chi-restraints excluded: chain D residue 743 TRP Chi-restraints excluded: chain D residue 749 VAL 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 1151 ILE 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 336 optimal weight: 0.8980 chunk 512 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 275 optimal weight: 9.9990 chunk 404 optimal weight: 50.0000 chunk 31 optimal weight: 0.5980 chunk 421 optimal weight: 20.0000 chunk 209 optimal weight: 10.0000 chunk 146 optimal weight: 0.0670 chunk 179 optimal weight: 4.9990 overall best weight: 1.9122 ------------------------------------------------------------------------------- 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** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 HIS ** C 495 ASN ** 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 D 446 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.186316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122096 restraints weight = 89606.555| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 4.33 r_work: 0.3586 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41920 Z= 0.148 Angle : 0.677 13.270 57244 Z= 0.340 Chirality : 0.042 0.205 6580 Planarity : 0.004 0.056 7264 Dihedral : 6.561 56.457 6162 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.20 % Favored : 90.72 % Rotamer: Outliers : 2.80 % Allowed : 19.22 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.12), residues: 5368 helix: 0.84 (0.11), residues: 2480 sheet: -0.48 (0.24), residues: 416 loop : -2.44 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 555 TYR 0.018 0.001 TYR A 833 PHE 0.022 0.001 PHE B 914 TRP 0.065 0.002 TRP D 868 HIS 0.018 0.001 HIS B 912 Details of bonding type rmsd covalent geometry : bond 0.00346 (41920) covalent geometry : angle 0.67651 (57244) hydrogen bonds : bond 0.03740 ( 1710) hydrogen bonds : angle 4.37674 ( 4926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14862.37 seconds wall clock time: 254 minutes 10.03 seconds (15250.03 seconds total)