Starting phenix.real_space_refine on Sun Jun 29 12:58:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9keu_62294/06_2025/9keu_62294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9keu_62294/06_2025/9keu_62294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9keu_62294/06_2025/9keu_62294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9keu_62294/06_2025/9keu_62294.map" model { file = "/net/cci-nas-00/data/ceres_data/9keu_62294/06_2025/9keu_62294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9keu_62294/06_2025/9keu_62294.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3795 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 154 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 19280 2.51 5 N 5601 2.21 5 O 6324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31457 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1759 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 8548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8548 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 9879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9879 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1207} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1601 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "G" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1569 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "F" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2529 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19076 SG CYS D 891 28.362 75.315 95.088 1.00 98.76 S ATOM 19643 SG CYS D 968 31.411 77.113 95.904 1.00101.77 S ATOM 19703 SG CYS D 978 29.307 78.608 93.724 1.00 94.01 S ATOM 12520 SG CYS D 60 89.851 58.877 119.510 1.00125.95 S ATOM 12538 SG CYS D 62 91.280 58.690 122.141 1.00129.86 S ATOM 12647 SG CYS D 75 88.232 56.290 122.632 1.00125.31 S ATOM 12673 SG CYS D 78 87.695 59.787 122.380 1.00123.11 S Time building chain proxies: 16.01, per 1000 atoms: 0.51 Number of scatterers: 31457 At special positions: 0 Unit cell: (152.4, 163.2, 200.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 95 16.00 P 154 15.00 Mg 1 11.99 O 6324 8.00 N 5601 7.00 C 19280 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: 7.37 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " Number of angles added : 6 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6716 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 49 sheets defined 42.9% alpha, 15.2% beta 51 base pairs and 111 stacking pairs defined. Time for finding SS restraints: 11.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.692A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.935A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.127A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.469A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 4.104A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.743A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.506A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 removed outlier: 3.658A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.021A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 removed outlier: 3.715A pdb=" N THR C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 290 through 301 removed outlier: 3.771A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 removed outlier: 3.813A pdb=" N VAL C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.686A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.757A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.562A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 534 through 539 removed outlier: 4.167A pdb=" N ARG C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 534 through 539' Processing helix chain 'C' and resid 589 through 593 removed outlier: 3.712A pdb=" N MET C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 3.888A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.269A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 removed outlier: 4.099A pdb=" N ALA C 823 " --> pdb=" O ARG C 819 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.629A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 927 removed outlier: 3.810A pdb=" N MET C 926 " --> pdb=" O PRO C 923 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN C 927 " --> pdb=" O ARG C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.638A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 959 removed outlier: 4.345A pdb=" N ARG C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 959 " --> pdb=" O TRP C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1037 through 1041 removed outlier: 3.866A pdb=" N ILE C1041 " --> pdb=" O ASP C1038 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1091 Processing helix chain 'C' and resid 1095 through 1109 Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.613A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.250A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 185 removed outlier: 3.727A pdb=" N GLU D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.644A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.509A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.080A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.576A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 3.914A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.914A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 478 removed outlier: 3.936A pdb=" N ARG D 474 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.362A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 490 " --> pdb=" O VAL D 486 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.699A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 removed outlier: 3.622A pdb=" N ARG D 624 " --> pdb=" O MET D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 677 removed outlier: 3.950A pdb=" N LEU D 677 " --> pdb=" O PHE D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 727 removed outlier: 3.600A pdb=" N ASP D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 763 Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.610A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 865 " --> pdb=" O ALA D 861 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.841A pdb=" N THR D 967 " --> pdb=" O SER D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1006 through 1010 removed outlier: 3.626A pdb=" N LEU D1010 " --> pdb=" O GLY D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1144 removed outlier: 3.578A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Proline residue: D1127 - end of helix removed outlier: 4.049A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D1132 " --> pdb=" O ARG D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.216A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1194 Processing helix chain 'D' and resid 1209 through 1216 Processing helix chain 'D' and resid 1219 through 1225 removed outlier: 3.763A pdb=" N ALA D1223 " --> pdb=" O SER D1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.739A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.652A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.708A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 removed outlier: 3.513A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 277 Processing helix chain 'F' and resid 278 through 308 removed outlier: 5.252A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 303 " --> pdb=" O ASN F 299 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS F 308 " --> pdb=" O VAL F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 335 removed outlier: 3.541A pdb=" N LEU F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU F 333 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS F 334 " --> pdb=" O ARG F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.615A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA F 363 " --> pdb=" O MET F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 removed outlier: 4.249A pdb=" N GLN F 388 " --> pdb=" O ARG F 384 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 404 removed outlier: 3.806A pdb=" N LEU F 399 " --> pdb=" O THR F 395 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 418 removed outlier: 3.834A pdb=" N ARG F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 439 Processing helix chain 'F' and resid 448 through 467 removed outlier: 3.531A pdb=" N THR F 466 " --> pdb=" O SER F 462 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 Processing helix chain 'J' and resid 175 through 188 Processing helix chain 'J' and resid 194 through 202 Processing helix chain 'J' and resid 211 through 225 removed outlier: 4.294A pdb=" N GLU J 215 " --> pdb=" O VAL J 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 194 through 202 Processing helix chain 'K' and resid 211 through 225 removed outlier: 4.172A pdb=" N GLU K 215 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 188 removed outlier: 3.662A pdb=" N LEU M 181 " --> pdb=" O THR M 177 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU M 182 " --> pdb=" O GLU M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 202 Processing helix chain 'M' and resid 211 through 225 removed outlier: 3.836A pdb=" N GLU M 215 " --> pdb=" O VAL M 211 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE M 225 " --> pdb=" O LEU M 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 188 Processing helix chain 'I' and resid 194 through 202 Processing helix chain 'I' and resid 211 through 225 removed outlier: 3.783A pdb=" N GLU I 215 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 3.942A pdb=" N VAL A 22 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 192 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.587A pdb=" N LEU A 138 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 136 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 99 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 134 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 50 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.587A pdb=" N LEU A 138 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 136 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 99 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 134 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.843A pdb=" N VAL A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.671A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 193 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR B 176 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP B 195 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 174 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU B 197 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 4.396A pdb=" N LYS B 99 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 134 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 5.928A pdb=" N GLY B 103 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR B 127 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.976A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.500A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.909A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.909A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.875A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 187 through 191 removed outlier: 4.835A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 7.298A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.897A pdb=" N ASP C 580 " --> pdb=" O ALA C 542 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 559 through 562 Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.941A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN C 700 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 648 through 653 removed outlier: 6.999A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC6, first strand: chain 'C' and resid 885 through 886 removed outlier: 8.276A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 885 through 886 Processing sheet with id=AC8, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.593A pdb=" N THR C 762 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 875 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 6.274A pdb=" N CYS D 441 " --> pdb=" O MET D 515 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 517 " --> pdb=" O CYS D 441 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 8.132A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD4, first strand: chain 'C' and resid 1133 through 1138 Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 7.198A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.728A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 233 through 235 removed outlier: 3.996A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.537A pdb=" N VAL D 899 " --> pdb=" O VAL D 960 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 929 through 930 removed outlier: 3.520A pdb=" N VAL D 938 " --> pdb=" O ALA D 929 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1051 through 1052 Processing sheet with id=AE3, first strand: chain 'D' and resid 1061 through 1066 removed outlier: 3.833A pdb=" N ILE D1080 " --> pdb=" O TYR D1062 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE D1064 " --> pdb=" O ASP D1078 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP D1078 " --> pdb=" O ILE D1064 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE D1066 " --> pdb=" O VAL D1076 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL D1076 " --> pdb=" O ILE D1066 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1180 through 1182 Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.713A pdb=" N ALA D1271 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN D1273 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU E 105 " --> pdb=" O GLN D1273 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 151 through 153 removed outlier: 3.542A pdb=" N GLU J 164 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 233 through 236 Processing sheet with id=AE8, first strand: chain 'K' and resid 151 through 153 Processing sheet with id=AE9, first strand: chain 'K' and resid 233 through 236 Processing sheet with id=AF1, first strand: chain 'M' and resid 151 through 153 removed outlier: 3.917A pdb=" N VAL M 165 " --> pdb=" O VAL M 172 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 192 through 193 Processing sheet with id=AF3, first strand: chain 'I' and resid 151 through 153 removed outlier: 4.511A pdb=" N VAL I 165 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 192 through 193 1249 hydrogen bonds defined for protein. 3525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 135 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 111 stacking parallelities Total time for adding SS restraints: 16.16 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10081 1.34 - 1.46: 6525 1.46 - 1.58: 15249 1.58 - 1.70: 306 1.70 - 1.82: 168 Bond restraints: 32329 Sorted by residual: bond pdb=" N VAL D 461 " pdb=" CA VAL D 461 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.06e+00 bond pdb=" N HIS K 234 " pdb=" CA HIS K 234 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.27e-02 6.20e+03 6.75e+00 bond pdb=" N LEU K 232 " pdb=" CA LEU K 232 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.26e-02 6.30e+03 6.64e+00 bond pdb=" N ARG A 186 " pdb=" CA ARG A 186 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.32e-02 5.74e+03 6.28e+00 bond pdb=" N GLU F 397 " pdb=" CA GLU F 397 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.02e+00 ... (remaining 32324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 44107 2.80 - 5.60: 325 5.60 - 8.40: 38 8.40 - 11.20: 10 11.20 - 14.01: 3 Bond angle restraints: 44483 Sorted by residual: angle pdb=" N VAL I 239 " pdb=" CA VAL I 239 " pdb=" C VAL I 239 " ideal model delta sigma weight residual 112.96 107.18 5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" N VAL M 239 " pdb=" CA VAL M 239 " pdb=" C VAL M 239 " ideal model delta sigma weight residual 113.71 108.83 4.88 9.50e-01 1.11e+00 2.64e+01 angle pdb=" CA ARG K 183 " pdb=" CB ARG K 183 " pdb=" CG ARG K 183 " ideal model delta sigma weight residual 114.10 123.96 -9.86 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CB MET C 393 " pdb=" CG MET C 393 " pdb=" SD MET C 393 " ideal model delta sigma weight residual 112.70 126.71 -14.01 3.00e+00 1.11e-01 2.18e+01 angle pdb=" N LEU B 60 " pdb=" CA LEU B 60 " pdb=" C LEU B 60 " ideal model delta sigma weight residual 114.62 109.49 5.13 1.14e+00 7.69e-01 2.02e+01 ... (remaining 44478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 18026 35.85 - 71.70: 1147 71.70 - 107.55: 53 107.55 - 143.40: 4 143.40 - 179.25: 7 Dihedral angle restraints: 19237 sinusoidal: 8796 harmonic: 10441 Sorted by residual: dihedral pdb=" CA ILE C1106 " pdb=" C ILE C1106 " pdb=" N VAL C1107 " pdb=" CA VAL C1107 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP C 126 " pdb=" C ASP C 126 " pdb=" N MET C 127 " pdb=" CA MET C 127 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA J 168 " pdb=" C ALA J 168 " pdb=" N GLY J 169 " pdb=" CA GLY J 169 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 19234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3892 0.047 - 0.093: 932 0.093 - 0.140: 234 0.140 - 0.186: 12 0.186 - 0.233: 6 Chirality restraints: 5076 Sorted by residual: chirality pdb=" CG LEU F 455 " pdb=" CB LEU F 455 " pdb=" CD1 LEU F 455 " pdb=" CD2 LEU F 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CG LEU F 460 " pdb=" CB LEU F 460 " pdb=" CD1 LEU F 460 " pdb=" CD2 LEU F 460 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU J 221 " pdb=" CB LEU J 221 " pdb=" CD1 LEU J 221 " pdb=" CD2 LEU J 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 5073 not shown) Planarity restraints: 5274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 170 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO J 171 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO J 171 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO J 171 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 205 " -0.029 2.00e-02 2.50e+03 2.23e-02 9.96e+00 pdb=" CG TYR K 205 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR K 205 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR K 205 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR K 205 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR K 205 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR K 205 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR K 205 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 656 " -0.010 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP D 656 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP D 656 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP D 656 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 656 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 656 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 656 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 656 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 656 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 656 " 0.016 2.00e-02 2.50e+03 ... (remaining 5271 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 318 2.56 - 3.14: 25725 3.14 - 3.73: 54299 3.73 - 4.31: 68599 4.31 - 4.90: 109695 Nonbonded interactions: 258636 Sorted by model distance: nonbonded pdb=" OD2 ASP D 539 " pdb="MG MG D2002 " model vdw 1.969 2.170 nonbonded pdb=" CA CYS D 968 " pdb="ZN ZN D2000 " model vdw 2.115 2.128 nonbonded pdb=" OG SER D1172 " pdb=" OE2 GLU D1199 " model vdw 2.200 3.040 nonbonded pdb=" O ASN D 468 " pdb=" OG SER D 471 " model vdw 2.206 3.040 nonbonded pdb=" O2 DC H 51 " pdb=" N2 DG G 27 " model vdw 2.208 2.496 ... (remaining 258631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 43 or (resid 144 and (name N or name CA or name C or name O or name CB )) or res \ id 145 through 152 or (resid 153 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 through 157 or (resid 158 and (name N or name \ CA or name C or name O or name CB )) or resid 159 through 160 or (resid 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 183 o \ r (resid 184 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 85 through 223 or (resid 224 and (name N or name CA or name C or name O or name \ CB )) or resid 225 through 226)) selection = (chain 'B' and resid 2 through 226) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 82.220 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 0.075 32336 Z= 0.186 Angle : 0.712 31.327 44489 Z= 0.373 Chirality : 0.043 0.233 5076 Planarity : 0.005 0.111 5274 Dihedral : 20.734 179.250 12521 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.70 % Favored : 95.27 % Rotamer: Outliers : 0.46 % Allowed : 29.09 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.14), residues: 3618 helix: 0.81 (0.14), residues: 1370 sheet: -0.61 (0.32), residues: 302 loop : -1.07 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 656 HIS 0.011 0.001 HIS M 201 PHE 0.021 0.001 PHE K 179 TYR 0.054 0.002 TYR K 205 ARG 0.018 0.001 ARG K 183 Details of bonding type rmsd hydrogen bonds : bond 0.17686 ( 1368) hydrogen bonds : angle 6.76284 ( 3787) metal coordination : bond 0.02184 ( 7) metal coordination : angle 17.74349 ( 6) covalent geometry : bond 0.00395 (32329) covalent geometry : angle 0.68188 (44483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 272 time to evaluate : 3.288 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 81 LYS cc_start: 0.9279 (ttmt) cc_final: 0.9017 (tppp) REVERT: B 168 TYR cc_start: 0.8645 (m-80) cc_final: 0.8407 (m-80) REVERT: C 127 MET cc_start: 0.8857 (pmm) cc_final: 0.8656 (pmm) REVERT: C 146 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: F 438 PHE cc_start: 0.9216 (m-10) cc_final: 0.8971 (m-10) REVERT: K 244 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8319 (tpp-160) REVERT: M 200 ASP cc_start: 0.7216 (m-30) cc_final: 0.6761 (p0) REVERT: I 185 PHE cc_start: 0.7076 (t80) cc_final: 0.6865 (t80) outliers start: 14 outliers final: 6 residues processed: 280 average time/residue: 0.4943 time to fit residues: 221.3404 Evaluate side-chains 263 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 256 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 201 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 156 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 826 ASN D1265 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.083623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.065904 restraints weight = 138695.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067407 restraints weight = 76650.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.068329 restraints weight = 52792.549| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 32336 Z= 0.261 Angle : 0.692 13.787 44489 Z= 0.367 Chirality : 0.045 0.176 5076 Planarity : 0.005 0.064 5274 Dihedral : 20.375 179.896 5679 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.72 % Allowed : 25.33 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.14), residues: 3618 helix: 0.77 (0.14), residues: 1390 sheet: -0.97 (0.28), residues: 356 loop : -1.12 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 656 HIS 0.007 0.001 HIS M 234 PHE 0.023 0.002 PHE K 185 TYR 0.018 0.002 TYR M 241 ARG 0.007 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.05789 ( 1368) hydrogen bonds : angle 5.23318 ( 3787) metal coordination : bond 0.00992 ( 7) metal coordination : angle 4.37464 ( 6) covalent geometry : bond 0.00587 (32329) covalent geometry : angle 0.69020 (44483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 265 time to evaluate : 3.580 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 12 ASP cc_start: 0.8433 (t0) cc_final: 0.8148 (t0) REVERT: A 81 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9111 (tppp) REVERT: B 168 TYR cc_start: 0.8979 (m-80) cc_final: 0.8345 (m-80) REVERT: B 189 PHE cc_start: 0.7972 (m-10) cc_final: 0.7750 (m-10) REVERT: B 191 LYS cc_start: 0.8472 (mttm) cc_final: 0.8269 (mttm) REVERT: B 219 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.6900 (t80) REVERT: C 440 MET cc_start: 0.8992 (tmm) cc_final: 0.8349 (tmm) REVERT: C 611 MET cc_start: 0.8411 (mpp) cc_final: 0.8178 (mpp) REVERT: C 913 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9219 (p) REVERT: C 1127 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 107 PHE cc_start: 0.8527 (t80) cc_final: 0.8193 (t80) REVERT: D 570 SER cc_start: 0.9016 (p) cc_final: 0.8673 (t) REVERT: D 820 MET cc_start: 0.7844 (tmm) cc_final: 0.7524 (ppp) REVERT: D 1012 MET cc_start: 0.6425 (pmm) cc_final: 0.6157 (mmt) REVERT: F 315 MET cc_start: 0.8332 (mtt) cc_final: 0.7708 (mtt) REVERT: J 212 ASN cc_start: 0.8859 (m-40) cc_final: 0.8542 (m-40) outliers start: 143 outliers final: 66 residues processed: 390 average time/residue: 0.4322 time to fit residues: 273.3334 Evaluate side-chains 306 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1071 MET Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1106 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 225 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 310 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 354 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 296 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 213 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 HIS ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.084742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067137 restraints weight = 137690.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068671 restraints weight = 75332.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069648 restraints weight = 51380.837| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32336 Z= 0.160 Angle : 0.627 11.853 44489 Z= 0.327 Chirality : 0.042 0.177 5076 Planarity : 0.004 0.057 5274 Dihedral : 20.276 176.893 5668 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.56 % Allowed : 26.35 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3618 helix: 0.86 (0.14), residues: 1393 sheet: -0.66 (0.31), residues: 305 loop : -1.16 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 656 HIS 0.011 0.001 HIS B 61 PHE 0.029 0.001 PHE K 185 TYR 0.023 0.001 TYR K 184 ARG 0.012 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 1368) hydrogen bonds : angle 4.91686 ( 3787) metal coordination : bond 0.00551 ( 7) metal coordination : angle 3.43027 ( 6) covalent geometry : bond 0.00361 (32329) covalent geometry : angle 0.62593 (44483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 275 time to evaluate : 3.464 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 81 LYS cc_start: 0.9352 (ttmt) cc_final: 0.9087 (tppp) REVERT: B 168 TYR cc_start: 0.8996 (m-80) cc_final: 0.8402 (m-80) REVERT: B 188 ASP cc_start: 0.6130 (t0) cc_final: 0.5798 (t70) REVERT: B 219 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.6526 (t80) REVERT: C 154 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8245 (mmm) REVERT: C 189 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7985 (tm-30) REVERT: C 197 LYS cc_start: 0.9293 (tptp) cc_final: 0.8896 (tptt) REVERT: C 440 MET cc_start: 0.9083 (tmm) cc_final: 0.8590 (tmm) REVERT: C 837 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 891 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8856 (p0) REVERT: D 173 ARG cc_start: 0.5904 (tpp-160) cc_final: 0.5629 (tpp-160) REVERT: D 203 ARG cc_start: 0.8481 (ttm170) cc_final: 0.8160 (mpt180) REVERT: D 217 ASP cc_start: 0.8362 (m-30) cc_final: 0.8128 (t0) REVERT: D 221 ASP cc_start: 0.9397 (m-30) cc_final: 0.8979 (m-30) REVERT: D 688 MET cc_start: 0.8571 (mmm) cc_final: 0.8250 (mmm) REVERT: D 820 MET cc_start: 0.7815 (tmm) cc_final: 0.7304 (tmm) REVERT: D 915 TYR cc_start: 0.8359 (m-10) cc_final: 0.8119 (m-10) REVERT: D 975 CYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8791 (p) REVERT: D 1012 MET cc_start: 0.6482 (pmm) cc_final: 0.6188 (mmt) REVERT: F 315 MET cc_start: 0.8272 (mtt) cc_final: 0.7937 (mtt) REVERT: F 372 MET cc_start: 0.8928 (mmm) cc_final: 0.8669 (mmm) REVERT: J 210 ASP cc_start: 0.6638 (p0) cc_final: 0.6232 (p0) REVERT: J 212 ASN cc_start: 0.8869 (m-40) cc_final: 0.8550 (m-40) REVERT: I 184 TYR cc_start: 0.7047 (t80) cc_final: 0.6829 (t80) REVERT: I 185 PHE cc_start: 0.7392 (t80) cc_final: 0.7122 (t80) REVERT: I 230 LYS cc_start: 0.7439 (tppt) cc_final: 0.6984 (tptp) outliers start: 108 outliers final: 55 residues processed: 368 average time/residue: 0.4286 time to fit residues: 256.7692 Evaluate side-chains 313 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 891 ASN Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 225 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain I residue 177 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 121 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 346 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 307 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.081230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063544 restraints weight = 139216.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064989 restraints weight = 76251.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.065884 restraints weight = 52404.634| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 32336 Z= 0.266 Angle : 0.695 14.245 44489 Z= 0.365 Chirality : 0.044 0.248 5076 Planarity : 0.005 0.055 5274 Dihedral : 20.341 179.227 5668 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.21 % Allowed : 26.06 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3618 helix: 0.75 (0.14), residues: 1400 sheet: -1.02 (0.28), residues: 368 loop : -1.24 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 211 HIS 0.008 0.002 HIS K 234 PHE 0.019 0.002 PHE D 107 TYR 0.020 0.002 TYR K 184 ARG 0.009 0.001 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.05480 ( 1368) hydrogen bonds : angle 4.97822 ( 3787) metal coordination : bond 0.00991 ( 7) metal coordination : angle 3.92919 ( 6) covalent geometry : bond 0.00597 (32329) covalent geometry : angle 0.69318 (44483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 260 time to evaluate : 3.337 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 81 LYS cc_start: 0.9404 (ttmt) cc_final: 0.9147 (tppp) REVERT: A 186 ARG cc_start: 0.7193 (mpt180) cc_final: 0.6851 (mmp-170) REVERT: B 168 TYR cc_start: 0.9108 (m-80) cc_final: 0.8851 (m-80) REVERT: B 188 ASP cc_start: 0.6372 (t0) cc_final: 0.6062 (t70) REVERT: C 127 MET cc_start: 0.8946 (pmm) cc_final: 0.8740 (pmm) REVERT: C 154 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8169 (mmt) REVERT: C 440 MET cc_start: 0.9141 (tmm) cc_final: 0.8603 (tmm) REVERT: C 837 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 1063 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7751 (t80) REVERT: C 1127 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8159 (mt-10) REVERT: D 49 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: D 173 ARG cc_start: 0.5769 (tpp-160) cc_final: 0.5552 (tpp-160) REVERT: D 217 ASP cc_start: 0.8370 (m-30) cc_final: 0.8130 (t0) REVERT: D 221 ASP cc_start: 0.9336 (m-30) cc_final: 0.8849 (m-30) REVERT: D 688 MET cc_start: 0.8250 (mmm) cc_final: 0.7727 (mmm) REVERT: D 820 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7249 (tmm) REVERT: D 975 CYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8758 (p) REVERT: D 1012 MET cc_start: 0.6482 (pmm) cc_final: 0.6156 (mmt) REVERT: F 281 MET cc_start: 0.8598 (mmm) cc_final: 0.8350 (mmm) REVERT: F 315 MET cc_start: 0.8266 (mtt) cc_final: 0.7892 (mtt) REVERT: J 174 LEU cc_start: 0.8972 (tp) cc_final: 0.8769 (tp) REVERT: J 212 ASN cc_start: 0.8861 (m-40) cc_final: 0.8350 (m-40) REVERT: J 234 HIS cc_start: 0.7241 (m90) cc_final: 0.6891 (m90) outliers start: 158 outliers final: 98 residues processed: 395 average time/residue: 0.4180 time to fit residues: 270.1181 Evaluate side-chains 342 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 238 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 860 LEU Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 490 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 225 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 141 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 259 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 363 optimal weight: 0.0010 chunk 337 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 HIS ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.083315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.065914 restraints weight = 136995.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067398 restraints weight = 74667.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068391 restraints weight = 51032.417| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32336 Z= 0.140 Angle : 0.627 14.149 44489 Z= 0.326 Chirality : 0.043 0.218 5076 Planarity : 0.004 0.069 5274 Dihedral : 20.254 174.990 5668 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.83 % Allowed : 27.74 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3618 helix: 0.89 (0.14), residues: 1398 sheet: -0.86 (0.28), residues: 361 loop : -1.15 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 166 HIS 0.007 0.001 HIS M 201 PHE 0.050 0.001 PHE K 185 TYR 0.026 0.001 TYR I 184 ARG 0.006 0.000 ARG J 150 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 1368) hydrogen bonds : angle 4.73447 ( 3787) metal coordination : bond 0.00371 ( 7) metal coordination : angle 2.39686 ( 6) covalent geometry : bond 0.00317 (32329) covalent geometry : angle 0.62626 (44483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 278 time to evaluate : 3.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9390 (ttmt) cc_final: 0.9115 (tppp) REVERT: A 186 ARG cc_start: 0.7160 (mpt180) cc_final: 0.6687 (mmp-170) REVERT: B 79 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.8996 (m110) REVERT: B 99 LYS cc_start: 0.6630 (pttm) cc_final: 0.6293 (pttt) REVERT: B 168 TYR cc_start: 0.9040 (m-80) cc_final: 0.8750 (m-80) REVERT: B 188 ASP cc_start: 0.6096 (t0) cc_final: 0.5798 (t0) REVERT: C 154 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8078 (mmt) REVERT: C 440 MET cc_start: 0.9168 (tmm) cc_final: 0.8590 (tmm) REVERT: C 837 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8566 (mp) REVERT: C 1063 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7760 (t80) REVERT: C 1127 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7953 (mt-10) REVERT: D 9 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: D 49 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: D 90 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 217 ASP cc_start: 0.8281 (m-30) cc_final: 0.8032 (t0) REVERT: D 221 ASP cc_start: 0.9324 (m-30) cc_final: 0.8813 (m-30) REVERT: D 688 MET cc_start: 0.8220 (mmm) cc_final: 0.7770 (mmm) REVERT: D 820 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7445 (ppp) REVERT: D 866 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7961 (ttp80) REVERT: D 975 CYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8753 (p) REVERT: F 281 MET cc_start: 0.8726 (mmm) cc_final: 0.8446 (mmm) REVERT: F 315 MET cc_start: 0.8196 (mtt) cc_final: 0.7937 (mtt) REVERT: F 372 MET cc_start: 0.8893 (mmm) cc_final: 0.8661 (tpp) REVERT: J 210 ASP cc_start: 0.6835 (p0) cc_final: 0.6466 (p0) REVERT: J 212 ASN cc_start: 0.8854 (m-40) cc_final: 0.8533 (m-40) REVERT: I 230 LYS cc_start: 0.7421 (tppt) cc_final: 0.6929 (tptp) outliers start: 116 outliers final: 69 residues processed: 377 average time/residue: 0.4942 time to fit residues: 306.7649 Evaluate side-chains 327 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 249 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 225 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 228 optimal weight: 4.9990 chunk 191 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 131 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 298 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 HIS ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.084251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.067056 restraints weight = 135375.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068588 restraints weight = 75248.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069466 restraints weight = 51836.924| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32336 Z= 0.147 Angle : 0.619 12.033 44489 Z= 0.324 Chirality : 0.042 0.215 5076 Planarity : 0.004 0.084 5274 Dihedral : 20.199 176.314 5668 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.09 % Allowed : 27.14 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3618 helix: 0.93 (0.14), residues: 1399 sheet: -0.64 (0.29), residues: 353 loop : -1.12 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 166 HIS 0.007 0.001 HIS M 201 PHE 0.043 0.001 PHE B 189 TYR 0.026 0.001 TYR K 184 ARG 0.017 0.000 ARG J 150 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 1368) hydrogen bonds : angle 4.66566 ( 3787) metal coordination : bond 0.00434 ( 7) metal coordination : angle 2.64547 ( 6) covalent geometry : bond 0.00335 (32329) covalent geometry : angle 0.61813 (44483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 265 time to evaluate : 3.482 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 130 ASP cc_start: 0.8723 (m-30) cc_final: 0.8489 (p0) REVERT: A 186 ARG cc_start: 0.7059 (mpt180) cc_final: 0.6754 (mmp-170) REVERT: B 168 TYR cc_start: 0.9002 (m-80) cc_final: 0.8730 (m-80) REVERT: B 188 ASP cc_start: 0.6152 (t0) cc_final: 0.5869 (t0) REVERT: C 127 MET cc_start: 0.8973 (pmm) cc_final: 0.8647 (pmm) REVERT: C 154 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8067 (mmt) REVERT: C 440 MET cc_start: 0.9173 (tmm) cc_final: 0.8542 (tmm) REVERT: C 837 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8457 (mp) REVERT: C 1063 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7765 (t80) REVERT: C 1127 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 49 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: D 90 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 173 ARG cc_start: 0.5845 (tpp-160) cc_final: 0.5609 (tpp-160) REVERT: D 217 ASP cc_start: 0.8271 (m-30) cc_final: 0.8015 (t0) REVERT: D 221 ASP cc_start: 0.9292 (m-30) cc_final: 0.8723 (m-30) REVERT: D 693 GLN cc_start: 0.8868 (mp10) cc_final: 0.8366 (mp10) REVERT: D 820 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7386 (ppp) REVERT: D 975 CYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8721 (p) REVERT: D 1113 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: F 281 MET cc_start: 0.8863 (mmm) cc_final: 0.8536 (mmm) REVERT: F 315 MET cc_start: 0.8241 (mtt) cc_final: 0.7953 (mtt) REVERT: F 372 MET cc_start: 0.8914 (mmm) cc_final: 0.8713 (tpp) REVERT: I 230 LYS cc_start: 0.7300 (tppt) cc_final: 0.6906 (tptp) outliers start: 124 outliers final: 78 residues processed: 364 average time/residue: 0.4322 time to fit residues: 255.6467 Evaluate side-chains 334 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 249 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 737 LEU Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 344 optimal weight: 6.9990 chunk 288 optimal weight: 0.1980 chunk 180 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 293 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 334 optimal weight: 8.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.080711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063125 restraints weight = 138034.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.064569 restraints weight = 76005.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065504 restraints weight = 52336.285| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 32336 Z= 0.238 Angle : 0.683 13.821 44489 Z= 0.357 Chirality : 0.044 0.200 5076 Planarity : 0.005 0.057 5274 Dihedral : 20.261 177.512 5668 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.42 % Allowed : 27.37 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3618 helix: 0.86 (0.14), residues: 1406 sheet: -0.83 (0.28), residues: 361 loop : -1.13 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 166 HIS 0.007 0.001 HIS K 234 PHE 0.054 0.002 PHE K 185 TYR 0.022 0.002 TYR K 184 ARG 0.008 0.000 ARG J 150 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 1368) hydrogen bonds : angle 4.81428 ( 3787) metal coordination : bond 0.00906 ( 7) metal coordination : angle 3.40726 ( 6) covalent geometry : bond 0.00536 (32329) covalent geometry : angle 0.68142 (44483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 250 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8831 (m-30) cc_final: 0.8572 (p0) REVERT: A 186 ARG cc_start: 0.7112 (mpt180) cc_final: 0.6590 (mmp-170) REVERT: B 168 TYR cc_start: 0.9012 (m-80) cc_final: 0.8668 (m-80) REVERT: B 213 LYS cc_start: 0.8951 (tmtt) cc_final: 0.8731 (tmtt) REVERT: B 226 ASN cc_start: 0.8854 (m-40) cc_final: 0.8175 (t0) REVERT: C 154 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8113 (mmt) REVERT: C 197 LYS cc_start: 0.9219 (tptp) cc_final: 0.8984 (tptp) REVERT: C 379 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7980 (mtp85) REVERT: C 440 MET cc_start: 0.9208 (tmm) cc_final: 0.8575 (tmm) REVERT: C 837 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8548 (mp) REVERT: C 1063 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7693 (t80) REVERT: C 1127 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8093 (mt-10) REVERT: D 9 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: D 49 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: D 90 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7812 (tm-30) REVERT: D 217 ASP cc_start: 0.8331 (m-30) cc_final: 0.8059 (t0) REVERT: D 221 ASP cc_start: 0.9291 (m-30) cc_final: 0.8761 (m-30) REVERT: D 693 GLN cc_start: 0.8869 (mp10) cc_final: 0.8579 (mp10) REVERT: D 715 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9042 (mtpp) REVERT: D 820 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7521 (ppp) REVERT: D 975 CYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8748 (p) REVERT: D 1113 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: E 66 ASP cc_start: 0.8799 (m-30) cc_final: 0.8589 (m-30) REVERT: F 281 MET cc_start: 0.8869 (mmm) cc_final: 0.8548 (mmm) REVERT: F 315 MET cc_start: 0.8227 (mtt) cc_final: 0.7903 (mtt) REVERT: J 234 HIS cc_start: 0.7228 (m90) cc_final: 0.6807 (m90) REVERT: J 244 ARG cc_start: 0.6772 (mmt180) cc_final: 0.6426 (mmt180) outliers start: 134 outliers final: 94 residues processed: 362 average time/residue: 0.4263 time to fit residues: 251.5068 Evaluate side-chains 344 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 240 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 313 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 291 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 246 optimal weight: 30.0000 chunk 334 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 359 optimal weight: 0.0970 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.083085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066062 restraints weight = 137496.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067508 restraints weight = 75542.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068397 restraints weight = 52139.881| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32336 Z= 0.156 Angle : 0.640 12.145 44489 Z= 0.332 Chirality : 0.042 0.220 5076 Planarity : 0.004 0.055 5274 Dihedral : 20.232 175.478 5668 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.92 % Allowed : 28.17 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3618 helix: 0.96 (0.14), residues: 1396 sheet: -0.74 (0.28), residues: 368 loop : -1.08 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 166 HIS 0.008 0.001 HIS M 201 PHE 0.048 0.001 PHE K 185 TYR 0.022 0.001 TYR K 184 ARG 0.012 0.000 ARG D 198 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1368) hydrogen bonds : angle 4.66108 ( 3787) metal coordination : bond 0.00495 ( 7) metal coordination : angle 2.41299 ( 6) covalent geometry : bond 0.00356 (32329) covalent geometry : angle 0.63950 (44483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 256 time to evaluate : 3.226 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 130 ASP cc_start: 0.8788 (m-30) cc_final: 0.8409 (p0) REVERT: A 186 ARG cc_start: 0.7143 (mpt180) cc_final: 0.6846 (mmp-170) REVERT: B 168 TYR cc_start: 0.8988 (m-80) cc_final: 0.8684 (m-80) REVERT: B 188 ASP cc_start: 0.5761 (t0) cc_final: 0.5399 (m-30) REVERT: B 226 ASN cc_start: 0.8800 (m-40) cc_final: 0.8273 (t0) REVERT: C 154 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8050 (mmt) REVERT: C 197 LYS cc_start: 0.9231 (tptp) cc_final: 0.8969 (tptp) REVERT: C 234 VAL cc_start: 0.8655 (m) cc_final: 0.8453 (m) REVERT: C 379 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7811 (mtp85) REVERT: C 440 MET cc_start: 0.9222 (tmm) cc_final: 0.8639 (tmm) REVERT: C 767 GLU cc_start: 0.8723 (mp0) cc_final: 0.8503 (mm-30) REVERT: C 837 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8525 (mp) REVERT: C 1063 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7814 (t80) REVERT: C 1127 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 9 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7920 (mm-30) REVERT: D 49 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8035 (mm-30) REVERT: D 90 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 217 ASP cc_start: 0.8302 (m-30) cc_final: 0.8017 (t0) REVERT: D 221 ASP cc_start: 0.9257 (m-30) cc_final: 0.8647 (m-30) REVERT: D 820 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7451 (ppp) REVERT: D 975 CYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8710 (p) REVERT: D 1112 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7273 (tpp) REVERT: D 1113 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: E 66 ASP cc_start: 0.8741 (m-30) cc_final: 0.8502 (m-30) REVERT: F 220 GLU cc_start: 0.8390 (pp20) cc_final: 0.8023 (pp20) REVERT: F 281 MET cc_start: 0.8872 (mmm) cc_final: 0.8546 (mmm) REVERT: F 315 MET cc_start: 0.8178 (mtt) cc_final: 0.7948 (mtt) REVERT: J 234 HIS cc_start: 0.7155 (m90) cc_final: 0.6689 (m90) REVERT: J 244 ARG cc_start: 0.6668 (mmt180) cc_final: 0.6431 (mmt180) outliers start: 119 outliers final: 90 residues processed: 353 average time/residue: 0.4694 time to fit residues: 270.1434 Evaluate side-chains 345 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 245 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 645 GLU Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 824 VAL Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 271 GLU Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 26 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 243 optimal weight: 3.9990 chunk 322 optimal weight: 9.9990 chunk 337 optimal weight: 0.9990 chunk 264 optimal weight: 40.0000 chunk 311 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.080337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063151 restraints weight = 137438.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064615 restraints weight = 76892.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065504 restraints weight = 53404.101| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32336 Z= 0.244 Angle : 0.698 12.988 44489 Z= 0.364 Chirality : 0.044 0.201 5076 Planarity : 0.005 0.057 5274 Dihedral : 20.264 177.023 5668 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.12 % Allowed : 28.17 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3618 helix: 0.87 (0.14), residues: 1403 sheet: -0.82 (0.28), residues: 365 loop : -1.13 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP M 166 HIS 0.008 0.001 HIS K 234 PHE 0.045 0.002 PHE B 189 TYR 0.026 0.002 TYR K 184 ARG 0.006 0.000 ARG J 244 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 1368) hydrogen bonds : angle 4.81873 ( 3787) metal coordination : bond 0.00921 ( 7) metal coordination : angle 3.37189 ( 6) covalent geometry : bond 0.00547 (32329) covalent geometry : angle 0.69702 (44483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 247 time to evaluate : 3.667 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 186 ARG cc_start: 0.7363 (mpt180) cc_final: 0.6860 (mmp-170) REVERT: B 188 ASP cc_start: 0.6223 (t0) cc_final: 0.5817 (m-30) REVERT: B 191 LYS cc_start: 0.8764 (mttm) cc_final: 0.8562 (mttm) REVERT: B 226 ASN cc_start: 0.8849 (m-40) cc_final: 0.8359 (t0) REVERT: C 197 LYS cc_start: 0.9185 (tptp) cc_final: 0.8913 (tptp) REVERT: C 379 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8006 (mtp85) REVERT: C 440 MET cc_start: 0.9225 (tmm) cc_final: 0.8613 (tmm) REVERT: C 837 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8524 (mp) REVERT: C 1063 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7721 (t80) REVERT: C 1127 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8050 (mt-10) REVERT: D 9 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: D 49 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: D 90 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7879 (tm-30) REVERT: D 217 ASP cc_start: 0.8313 (m-30) cc_final: 0.8028 (t0) REVERT: D 221 ASP cc_start: 0.9281 (m-30) cc_final: 0.8707 (m-30) REVERT: D 715 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.9044 (mtpp) REVERT: D 820 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7220 (tmm) REVERT: D 975 CYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8699 (p) REVERT: D 1112 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7421 (tpp) REVERT: D 1113 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: F 220 GLU cc_start: 0.8365 (pp20) cc_final: 0.8006 (pp20) REVERT: F 281 MET cc_start: 0.8866 (mmm) cc_final: 0.8558 (mmm) REVERT: F 315 MET cc_start: 0.8209 (mtt) cc_final: 0.7905 (mtt) outliers start: 125 outliers final: 103 residues processed: 351 average time/residue: 0.5140 time to fit residues: 289.2932 Evaluate side-chains 349 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 236 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 168 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 841 HIS Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1073 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 302 PHE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 866 ARG Chi-restraints excluded: chain D residue 935 ASN Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1168 ILE Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 206 optimal weight: 0.8980 chunk 334 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 150 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 chunk 250 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 188 optimal weight: 0.0980 chunk 252 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 HIS D 687 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.083347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.066120 restraints weight = 138867.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067635 restraints weight = 76040.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068608 restraints weight = 52436.204| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32336 Z= 0.129 Angle : 0.661 14.699 44489 Z= 0.337 Chirality : 0.043 0.289 5076 Planarity : 0.004 0.060 5274 Dihedral : 20.157 177.119 5668 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.00 % Allowed : 29.25 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3618 helix: 0.92 (0.14), residues: 1397 sheet: -0.71 (0.28), residues: 368 loop : -1.03 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP M 166 HIS 0.010 0.001 HIS M 201 PHE 0.045 0.001 PHE K 185 TYR 0.028 0.001 TYR K 184 ARG 0.013 0.000 ARG K 183 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 1368) hydrogen bonds : angle 4.59382 ( 3787) metal coordination : bond 0.00256 ( 7) metal coordination : angle 1.98466 ( 6) covalent geometry : bond 0.00291 (32329) covalent geometry : angle 0.66063 (44483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 276 time to evaluate : 3.775 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 186 ARG cc_start: 0.7213 (mpt180) cc_final: 0.6907 (mmp-170) REVERT: B 168 TYR cc_start: 0.8926 (m-80) cc_final: 0.8599 (m-80) REVERT: B 188 ASP cc_start: 0.5764 (t0) cc_final: 0.5541 (m-30) REVERT: B 226 ASN cc_start: 0.8669 (m-40) cc_final: 0.8453 (t0) REVERT: C 197 LYS cc_start: 0.9230 (tptp) cc_final: 0.8934 (tptp) REVERT: C 234 VAL cc_start: 0.8579 (m) cc_final: 0.8345 (m) REVERT: C 379 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7741 (mtp85) REVERT: C 440 MET cc_start: 0.9241 (tmm) cc_final: 0.8690 (tmm) REVERT: C 837 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8612 (mp) REVERT: C 1063 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7816 (t80) REVERT: C 1127 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7899 (mt-10) REVERT: D 9 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: D 49 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: D 90 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7799 (tm-30) REVERT: D 198 ARG cc_start: 0.4756 (OUTLIER) cc_final: 0.4552 (mmt-90) REVERT: D 217 ASP cc_start: 0.8338 (m-30) cc_final: 0.8033 (t0) REVERT: D 221 ASP cc_start: 0.9335 (m-30) cc_final: 0.8852 (m-30) REVERT: D 820 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7549 (ppp) REVERT: D 975 CYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8771 (p) REVERT: D 1112 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7380 (tpp) REVERT: D 1113 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: F 220 GLU cc_start: 0.8320 (pp20) cc_final: 0.8006 (pp20) REVERT: F 281 MET cc_start: 0.8911 (mmm) cc_final: 0.8650 (mmm) REVERT: F 526 TYR cc_start: 0.6622 (t80) cc_final: 0.6406 (t80) REVERT: J 155 ASP cc_start: 0.8167 (p0) cc_final: 0.7953 (p0) outliers start: 91 outliers final: 61 residues processed: 353 average time/residue: 0.5604 time to fit residues: 319.0050 Evaluate side-chains 321 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 250 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 182 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 986 GLN Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 198 ARG Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 820 MET Chi-restraints excluded: chain D residue 975 CYS Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1113 GLU Chi-restraints excluded: chain D residue 1248 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 312 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 341 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 HIS ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.080190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062995 restraints weight = 140757.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064445 restraints weight = 78154.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.065315 restraints weight = 54216.154| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32336 Z= 0.232 Angle : 0.712 13.925 44489 Z= 0.368 Chirality : 0.044 0.239 5076 Planarity : 0.005 0.089 5274 Dihedral : 20.169 177.254 5665 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.10 % Allowed : 29.25 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3618 helix: 0.85 (0.14), residues: 1403 sheet: -0.66 (0.29), residues: 350 loop : -1.10 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M 166 HIS 0.007 0.001 HIS M 201 PHE 0.047 0.002 PHE B 189 TYR 0.032 0.002 TYR K 184 ARG 0.013 0.001 ARG K 183 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 1368) hydrogen bonds : angle 4.77165 ( 3787) metal coordination : bond 0.00867 ( 7) metal coordination : angle 3.41180 ( 6) covalent geometry : bond 0.00522 (32329) covalent geometry : angle 0.71064 (44483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11040.50 seconds wall clock time: 194 minutes 57.45 seconds (11697.45 seconds total)