Starting phenix.real_space_refine on Mon Jul 6 12:44:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ji4_61495/07_2026/9ji4_61495.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ji4_61495/07_2026/9ji4_61495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ji4_61495/07_2026/9ji4_61495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ji4_61495/07_2026/9ji4_61495.map" model { file = "/net/cci-nas-00/data/ceres_data/9ji4_61495/07_2026/9ji4_61495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ji4_61495/07_2026/9ji4_61495.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} 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: 6.55, per 1000 atoms: 0.21 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 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: 3.91 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: 8.10 Time building geometry restraints manager: 3.54 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=" C3' DG H 15 " pdb=" C2' DG H 15 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT G 74 " pdb=" C2' DT G 74 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT H 1 " pdb=" C2' DT H 1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA G 21 " pdb=" C2' DA G 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.95e+00 bond pdb=" C3' DC H 51 " pdb=" C2' DC H 51 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 ... (remaining 32324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 44082 2.80 - 5.60: 350 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=" O4' DG G 2 " pdb=" C4' DG G 2 " pdb=" C3' DG G 2 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O4' DA G 57 " pdb=" C4' DA G 57 " pdb=" C3' DA G 57 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+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: 3754 0.047 - 0.093: 1026 0.093 - 0.140: 272 0.140 - 0.186: 18 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 36.200 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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= 0.295 Angle : 0.744 31.327 44489 Z= 0.459 Chirality : 0.045 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 : 16.55 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.018 0.001 ARG K 183 TYR 0.054 0.002 TYR K 205 PHE 0.021 0.001 PHE K 179 TRP 0.042 0.002 TRP D 656 HIS 0.011 0.001 HIS M 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.30 (32329) covalent geometry : angle 0.71478 / 0.46 (44483) hydrogen bonds : bond 0.17686 / 11.91 ( 1368) hydrogen bonds : angle 6.76284 / 4.67 ( 3787) metal coordination : bond 0.02184 / 1.09 ( 7) metal coordination : angle 17.74349 / 5.72 ( 6) *********************** 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 343 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 329 time to evaluate : 1.196 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: 0.9278 (ttmt) cc_final: 0.9061 (tppp) REVERT: B 168 TYR cc_start: 0.8405 (m-80) cc_final: 0.8073 (m-80) REVERT: B 185 GLN cc_start: 0.7027 (tp40) cc_final: 0.6750 (tp-100) REVERT: C 146 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: C 197 LYS cc_start: 0.9200 (tptp) cc_final: 0.8810 (tptt) REVERT: D 376 GLU cc_start: 0.8335 (tp30) cc_final: 0.8000 (tp30) REVERT: D 379 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7491 (p0) REVERT: K 221 LEU cc_start: 0.9512 (mm) cc_final: 0.9190 (mm) REVERT: K 229 GLU cc_start: 0.8862 (mp0) cc_final: 0.8622 (mm-30) REVERT: M 153 PHE cc_start: 0.5574 (t80) cc_final: 0.4946 (t80) REVERT: M 195 LYS cc_start: 0.8440 (mptt) cc_final: 0.7830 (mmmt) REVERT: M 230 LYS cc_start: 0.6778 (tptp) cc_final: 0.6274 (mmmm) outliers start: 14 outliers final: 5 residues processed: 336 average time/residue: 0.2075 time to fit residues: 112.4760 Evaluate side-chains 289 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 282 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 D residue 379 ASP Chi-restraints excluded: chain F residue 514 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 30.0000 overall best weight: 2.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN C1129 GLN ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1265 ASN ** K 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.092125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.065569 restraints weight = 117221.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.067494 restraints weight = 58692.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068746 restraints weight = 38270.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.069425 restraints weight = 29355.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.069936 restraints weight = 25227.751| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0962 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= 0.187 Angle : 0.668 11.705 44489 Z= 0.359 Chirality : 0.045 0.225 5076 Planarity : 0.005 0.067 5274 Dihedral : 20.284 175.954 5679 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.53 % Allowed : 26.29 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.14), residues: 3618 helix: 0.82 (0.14), residues: 1396 sheet: -0.86 (0.29), residues: 356 loop : -1.07 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 244 TYR 0.047 0.002 TYR K 220 PHE 0.025 0.002 PHE K 179 TRP 0.028 0.002 TRP M 203 HIS 0.006 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (32329) covalent geometry : angle 0.66487 / 0.36 (44483) hydrogen bonds : bond 0.05846 / 4.14 ( 1368) hydrogen bonds : angle 5.37002 / 3.74 ( 3787) metal coordination : bond 0.00783 / 0.39 ( 7) metal coordination : angle 5.61102 / 1.95 ( 6) *********************** 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 409 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 302 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9281 (ttmt) cc_final: 0.9070 (tppp) REVERT: A 130 ASP cc_start: 0.8663 (m-30) cc_final: 0.8378 (p0) REVERT: B 168 TYR cc_start: 0.8583 (m-80) cc_final: 0.8055 (m-80) REVERT: C 197 LYS cc_start: 0.9215 (tptp) cc_final: 0.8829 (tptt) REVERT: C 818 GLU cc_start: 0.7643 (tp30) cc_final: 0.7406 (tm-30) REVERT: C 892 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8831 (mtmt) REVERT: D 376 GLU cc_start: 0.8431 (tp30) cc_final: 0.7958 (tp30) REVERT: D 379 ASP cc_start: 0.8263 (p0) cc_final: 0.7756 (p0) REVERT: D 820 MET cc_start: 0.7733 (tmm) cc_final: 0.7477 (tmm) REVERT: F 485 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: F 502 ARG cc_start: 0.7898 (mmp-170) cc_final: 0.7686 (mmp-170) REVERT: J 160 GLU cc_start: 0.8838 (tp30) cc_final: 0.8597 (tm-30) REVERT: J 199 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8815 (mp) REVERT: K 212 ASN cc_start: 0.9035 (m110) cc_final: 0.8413 (t0) REVERT: K 221 LEU cc_start: 0.9440 (mm) cc_final: 0.9217 (mm) REVERT: K 229 GLU cc_start: 0.8680 (mp0) cc_final: 0.8369 (mm-30) outliers start: 107 outliers final: 51 residues processed: 391 average time/residue: 0.1881 time to fit residues: 119.5801 Evaluate side-chains 324 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 66 VAL Chi-restraints excluded: chain B residue 69 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 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 399 VAL Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 497 ILE Chi-restraints excluded: chain C residue 500 LEU 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 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 892 LYS Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1073 CYS 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 92 MET Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 570 SER Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 796 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain M residue 225 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 53 optimal weight: 0.8980 chunk 321 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 257 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 HIS ** B 79 ASN ** 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** C 610 ASN ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN D 826 ASN ** D 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.091085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.064863 restraints weight = 118570.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.066717 restraints weight = 59051.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067928 restraints weight = 38411.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068587 restraints weight = 29448.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.069084 restraints weight = 25377.711| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32336 Z= 0.222 Angle : 0.672 11.785 44489 Z= 0.359 Chirality : 0.045 0.272 5076 Planarity : 0.005 0.054 5274 Dihedral : 20.272 175.717 5668 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.68 % Allowed : 25.82 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3618 helix: 0.78 (0.14), residues: 1397 sheet: -0.66 (0.31), residues: 304 loop : -1.22 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 183 TYR 0.037 0.002 TYR K 220 PHE 0.020 0.002 PHE K 185 TRP 0.034 0.002 TRP M 203 HIS 0.011 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (32329) covalent geometry : angle 0.67000 / 0.36 (44483) hydrogen bonds : bond 0.05309 / 3.74 ( 1368) hydrogen bonds : angle 5.09881 / 3.56 ( 3787) metal coordination : bond 0.00838 / 0.41 ( 7) metal coordination : angle 4.36677 / 1.38 ( 6) *********************** 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 426 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 284 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LYS cc_start: 0.9325 (ttmt) cc_final: 0.9119 (tppp) REVERT: A 130 ASP cc_start: 0.8725 (m-30) cc_final: 0.8473 (p0) REVERT: B 168 TYR cc_start: 0.8765 (m-80) cc_final: 0.8154 (m-80) REVERT: B 191 LYS cc_start: 0.8621 (mttm) cc_final: 0.8371 (mttm) REVERT: B 219 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.6920 (t80) REVERT: C 146 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: C 154 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8326 (mmm) REVERT: C 197 LYS cc_start: 0.9235 (tptp) cc_final: 0.8836 (tptt) REVERT: C 440 MET cc_start: 0.8731 (tmm) cc_final: 0.8332 (tmm) REVERT: C 483 MET cc_start: 0.9019 (ttt) cc_final: 0.8778 (ttp) REVERT: C 818 GLU cc_start: 0.7731 (tp30) cc_final: 0.7486 (tm-30) REVERT: C 837 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 49 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: D 90 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8054 (mp0) REVERT: D 107 PHE cc_start: 0.8476 (t80) cc_final: 0.8197 (t80) REVERT: D 376 GLU cc_start: 0.8488 (tp30) cc_final: 0.7991 (tp30) REVERT: D 379 ASP cc_start: 0.8377 (p0) cc_final: 0.7883 (p0) REVERT: D 820 MET cc_start: 0.7761 (tmm) cc_final: 0.7389 (ppp) REVERT: F 263 MET cc_start: 0.8782 (tmm) cc_final: 0.8507 (mtt) REVERT: F 485 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: J 158 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6191 (tp) REVERT: J 160 GLU cc_start: 0.8916 (tp30) cc_final: 0.8597 (tm-30) REVERT: K 151 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6467 (mt) REVERT: K 183 ARG cc_start: 0.8524 (tpt90) cc_final: 0.8314 (tpt90) REVERT: K 212 ASN cc_start: 0.8987 (m110) cc_final: 0.8337 (t0) REVERT: M 153 PHE cc_start: 0.6065 (t80) cc_final: 0.5304 (t80) REVERT: M 244 ARG cc_start: 0.6550 (mmp80) cc_final: 0.6203 (mmm160) outliers start: 142 outliers final: 77 residues processed: 402 average time/residue: 0.1906 time to fit residues: 125.2661 Evaluate side-chains 341 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 256 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 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 219 PHE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 224 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 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 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 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 1031 MET Chi-restraints excluded: chain C residue 1071 MET Chi-restraints excluded: chain C residue 1106 ILE 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 49 GLU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 204 GLU 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 496 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 570 SER 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 796 ASP Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 862 ASP 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 485 GLN Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 151 LEU Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 ILE 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 352 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 40 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN B 61 HIS ** C 232 GLN ** 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 ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 HIS K 188 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.091232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.065134 restraints weight = 117689.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.066976 restraints weight = 58363.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.068166 restraints weight = 37972.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.068823 restraints weight = 29156.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.069327 restraints weight = 25154.828| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1728 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= 0.175 Angle : 0.643 9.806 44489 Z= 0.343 Chirality : 0.045 0.285 5076 Planarity : 0.004 0.053 5274 Dihedral : 20.233 174.352 5668 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.82 % Allowed : 26.62 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3618 helix: 0.83 (0.14), residues: 1399 sheet: -0.87 (0.30), residues: 308 loop : -1.19 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1143 TYR 0.030 0.001 TYR D 915 PHE 0.028 0.002 PHE K 179 TRP 0.019 0.002 TRP M 166 HIS 0.008 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (32329) covalent geometry : angle 0.64204 / 0.34 (44483) hydrogen bonds : bond 0.04931 / 3.50 ( 1368) hydrogen bonds : angle 4.92075 / 3.45 ( 3787) metal coordination : bond 0.00584 / 0.29 ( 7) metal coordination : angle 3.29489 / 1.06 ( 6) *********************** 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 421 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 275 time to evaluate : 1.197 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: A 81 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9120 (tppp) REVERT: A 130 ASP cc_start: 0.8704 (m-30) cc_final: 0.8432 (p0) REVERT: B 168 TYR cc_start: 0.8862 (m-80) cc_final: 0.8258 (m-80) REVERT: B 191 LYS cc_start: 0.8626 (mttm) cc_final: 0.8369 (mttm) REVERT: B 219 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.6789 (t80) REVERT: C 154 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7979 (mmt) REVERT: C 197 LYS cc_start: 0.9243 (tptp) cc_final: 0.8809 (tptt) REVERT: C 228 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7844 (mpt180) REVERT: C 440 MET cc_start: 0.8846 (tmm) cc_final: 0.8167 (tmm) REVERT: C 483 MET cc_start: 0.9000 (ttt) cc_final: 0.8760 (ttp) REVERT: C 771 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7377 (ttt-90) REVERT: C 818 GLU cc_start: 0.7705 (tp30) cc_final: 0.7478 (tm-30) REVERT: C 837 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8470 (mp) REVERT: D 49 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: D 90 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8047 (mp0) REVERT: D 323 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8346 (mm-30) REVERT: D 376 GLU cc_start: 0.8531 (tp30) cc_final: 0.8021 (tp30) REVERT: D 379 ASP cc_start: 0.8304 (p0) cc_final: 0.7826 (p0) REVERT: D 820 MET cc_start: 0.7707 (tmm) cc_final: 0.7135 (tmm) REVERT: F 485 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: F 502 ARG cc_start: 0.7915 (mmp-170) cc_final: 0.7327 (tpp-160) REVERT: J 182 LEU cc_start: 0.9200 (tp) cc_final: 0.8963 (tp) REVERT: J 199 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8831 (mp) REVERT: K 159 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6302 (p0) REVERT: K 212 ASN cc_start: 0.8949 (m110) cc_final: 0.8268 (t0) REVERT: M 153 PHE cc_start: 0.6263 (t80) cc_final: 0.5273 (t80) REVERT: M 244 ARG cc_start: 0.6517 (mmp80) cc_final: 0.5951 (mmm-85) outliers start: 146 outliers final: 79 residues processed: 388 average time/residue: 0.1929 time to fit residues: 122.1275 Evaluate side-chains 345 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 257 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 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 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 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 363 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 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 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 907 LEU Chi-restraints excluded: chain C residue 919 THR 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 1071 MET Chi-restraints excluded: chain C residue 1125 LEU 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 49 GLU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 204 GLU 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 528 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 644 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 800 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 862 ASP 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 E residue 83 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 503 ILE Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 177 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 176 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 243 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 315 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 HIS ** 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 = 0.3800 r_free = 0.3800 target = 0.090888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.064774 restraints weight = 118247.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.066622 restraints weight = 58541.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067804 restraints weight = 38100.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068531 restraints weight = 29227.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.068907 restraints weight = 24939.976| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32336 Z= 0.182 Angle : 0.648 11.088 44489 Z= 0.345 Chirality : 0.045 0.293 5076 Planarity : 0.005 0.052 5274 Dihedral : 20.212 173.819 5668 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.58 % Allowed : 27.01 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3618 helix: 0.86 (0.14), residues: 1398 sheet: -1.08 (0.28), residues: 365 loop : -1.13 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 183 TYR 0.056 0.002 TYR K 220 PHE 0.036 0.002 PHE K 185 TRP 0.044 0.002 TRP I 166 HIS 0.008 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (32329) covalent geometry : angle 0.64700 / 0.35 (44483) hydrogen bonds : bond 0.04806 / 3.41 ( 1368) hydrogen bonds : angle 4.84802 / 3.39 ( 3787) metal coordination : bond 0.00585 / 0.29 ( 7) metal coordination : angle 3.17491 / 1.02 ( 6) *********************** 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 409 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 270 time to evaluate : 1.148 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: A 81 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9162 (tppp) REVERT: A 130 ASP cc_start: 0.8785 (m-30) cc_final: 0.8395 (p0) REVERT: B 168 TYR cc_start: 0.8883 (m-80) cc_final: 0.8254 (m-80) REVERT: B 191 LYS cc_start: 0.8584 (mttm) cc_final: 0.8319 (mttm) REVERT: B 219 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.6823 (t80) REVERT: C 154 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7994 (mmt) REVERT: C 396 MET cc_start: 0.8728 (tmm) cc_final: 0.8392 (tmm) REVERT: C 440 MET cc_start: 0.8914 (tmm) cc_final: 0.8389 (tmm) REVERT: C 483 MET cc_start: 0.9007 (ttt) cc_final: 0.8760 (ttp) REVERT: C 771 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7329 (ttt-90) REVERT: C 818 GLU cc_start: 0.7687 (tp30) cc_final: 0.7463 (tm-30) REVERT: C 837 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8554 (mp) REVERT: C 841 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7439 (m90) REVERT: C 1063 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7655 (t80) REVERT: D 49 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: D 90 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7998 (mp0) REVERT: D 323 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8394 (mm-30) REVERT: D 820 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7420 (ppp) REVERT: D 860 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9114 (mm) REVERT: F 263 MET cc_start: 0.8830 (tmm) cc_final: 0.8544 (mtt) REVERT: F 372 MET cc_start: 0.8956 (mmm) cc_final: 0.8659 (tpp) REVERT: F 485 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: F 502 ARG cc_start: 0.8106 (mmp-170) cc_final: 0.7381 (tpp-160) REVERT: J 158 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6443 (tp) REVERT: J 182 LEU cc_start: 0.9194 (tp) cc_final: 0.8960 (tp) REVERT: M 153 PHE cc_start: 0.6225 (t80) cc_final: 0.5258 (t80) REVERT: M 244 ARG cc_start: 0.6345 (mmp80) cc_final: 0.5666 (mmm-85) outliers start: 139 outliers final: 83 residues processed: 377 average time/residue: 0.1963 time to fit residues: 121.5541 Evaluate side-chains 352 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 258 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 146 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 171 VAL 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 224 VAL 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 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 748 THR Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 820 LEU 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 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 1071 MET 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 92 MET 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 422 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 528 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 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 733 MET Chi-restraints excluded: chain D residue 796 ASP 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 860 LEU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE 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 485 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 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 110 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 275 optimal weight: 0.6980 chunk 59 optimal weight: 0.0980 chunk 326 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 365 optimal weight: 8.9990 chunk 145 optimal weight: 0.0670 chunk 124 optimal weight: 9.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1042 HIS D 771 ASN M 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.092800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.066660 restraints weight = 116013.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.068582 restraints weight = 56842.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069844 restraints weight = 36608.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.070599 restraints weight = 27920.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.071001 restraints weight = 23677.683| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 32336 Z= 0.124 Angle : 0.627 10.626 44489 Z= 0.333 Chirality : 0.044 0.305 5076 Planarity : 0.004 0.065 5274 Dihedral : 20.135 173.286 5668 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.43 % Allowed : 28.46 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.14), residues: 3618 helix: 0.94 (0.14), residues: 1389 sheet: -0.56 (0.30), residues: 321 loop : -1.14 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 183 TYR 0.045 0.001 TYR K 220 PHE 0.016 0.001 PHE I 179 TRP 0.026 0.002 TRP M 166 HIS 0.007 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (32329) covalent geometry : angle 0.62616 / 0.33 (44483) hydrogen bonds : bond 0.04438 / 3.16 ( 1368) hydrogen bonds : angle 4.67481 / 3.27 ( 3787) metal coordination : bond 0.00196 / 0.09 ( 7) metal coordination : angle 1.99281 / 0.67 ( 6) *********************** 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 388 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 284 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8734 (m-30) cc_final: 0.8369 (p0) REVERT: B 168 TYR cc_start: 0.8804 (m-80) cc_final: 0.8205 (m-80) REVERT: B 219 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.6519 (t80) REVERT: C 154 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7910 (mmt) REVERT: C 387 ASN cc_start: 0.9254 (m-40) cc_final: 0.9050 (m-40) REVERT: C 396 MET cc_start: 0.8713 (tmm) cc_final: 0.8381 (tmm) REVERT: C 440 MET cc_start: 0.8933 (tmm) cc_final: 0.8369 (tmm) REVERT: C 771 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7279 (ttt-90) REVERT: C 818 GLU cc_start: 0.7543 (tp30) cc_final: 0.6955 (tm-30) REVERT: C 837 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8327 (mp) REVERT: D 49 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8013 (mm-30) REVERT: D 203 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8134 (mpt180) REVERT: D 323 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8355 (mm-30) REVERT: D 376 GLU cc_start: 0.8672 (tp30) cc_final: 0.8288 (tp30) REVERT: D 820 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7140 (tmm) REVERT: F 282 MET cc_start: 0.9039 (ttm) cc_final: 0.8723 (mmp) REVERT: F 485 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: F 502 ARG cc_start: 0.8099 (mmp-170) cc_final: 0.7419 (tpp-160) REVERT: J 182 LEU cc_start: 0.9099 (tp) cc_final: 0.8772 (tt) REVERT: J 197 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8460 (ttmt) REVERT: M 153 PHE cc_start: 0.5895 (t80) cc_final: 0.5138 (t80) REVERT: M 244 ARG cc_start: 0.6404 (mmp80) cc_final: 0.6015 (mmm160) outliers start: 104 outliers final: 63 residues processed: 363 average time/residue: 0.2008 time to fit residues: 119.5675 Evaluate side-chains 331 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 261 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 56 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 140 VAL 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 93 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 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 820 LEU 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 1073 CYS Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 14 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 298 VAL Chi-restraints excluded: chain D residue 441 CYS 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 733 MET Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 796 ASP 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 1064 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 213 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 291 optimal weight: 40.0000 chunk 15 optimal weight: 0.5980 chunk 303 optimal weight: 50.0000 chunk 30 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 HIS K 234 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.091257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065138 restraints weight = 117202.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066994 restraints weight = 58406.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068222 restraints weight = 37938.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068954 restraints weight = 29037.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.069417 restraints weight = 24746.691| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32336 Z= 0.170 Angle : 0.635 10.104 44489 Z= 0.337 Chirality : 0.044 0.301 5076 Planarity : 0.004 0.053 5274 Dihedral : 20.118 173.091 5666 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.69 % Allowed : 28.46 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3618 helix: 0.95 (0.14), residues: 1396 sheet: -0.84 (0.29), residues: 346 loop : -1.13 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 183 TYR 0.039 0.001 TYR K 220 PHE 0.027 0.002 PHE K 179 TRP 0.024 0.001 TRP M 166 HIS 0.007 0.001 HIS K 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (32329) covalent geometry : angle 0.63397 / 0.34 (44483) hydrogen bonds : bond 0.04581 / 3.24 ( 1368) hydrogen bonds : angle 4.66122 / 3.26 ( 3787) metal coordination : bond 0.00628 / 0.31 ( 7) metal coordination : angle 3.17848 / 1.01 ( 6) *********************** 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 373 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 261 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8769 (m-30) cc_final: 0.8396 (p0) REVERT: B 168 TYR cc_start: 0.8905 (m-80) cc_final: 0.8218 (m-80) REVERT: C 396 MET cc_start: 0.8730 (tmm) cc_final: 0.8372 (tmm) REVERT: C 440 MET cc_start: 0.8978 (tmm) cc_final: 0.8423 (tmm) REVERT: C 771 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7240 (ttt-90) REVERT: C 818 GLU cc_start: 0.7674 (tp30) cc_final: 0.7049 (tm-30) REVERT: C 837 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 1063 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7753 (t80) REVERT: D 323 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8378 (mm-30) REVERT: D 376 GLU cc_start: 0.8718 (tp30) cc_final: 0.8389 (tp30) REVERT: D 379 ASP cc_start: 0.8451 (p0) cc_final: 0.7942 (p0) REVERT: D 820 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7435 (ppp) REVERT: F 263 MET cc_start: 0.8829 (tmm) cc_final: 0.8561 (mtt) REVERT: F 485 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: F 502 ARG cc_start: 0.8026 (mmp-170) cc_final: 0.7390 (tpp-160) REVERT: J 201 HIS cc_start: 0.8817 (OUTLIER) cc_final: 0.8152 (t70) REVERT: M 153 PHE cc_start: 0.5974 (t80) cc_final: 0.5181 (t80) REVERT: M 244 ARG cc_start: 0.6504 (mmp80) cc_final: 0.6107 (mmm160) outliers start: 112 outliers final: 72 residues processed: 348 average time/residue: 0.1916 time to fit residues: 110.3865 Evaluate side-chains 331 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 253 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 95 MET 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 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 VAL 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 224 VAL Chi-restraints excluded: chain C residue 244 THR 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 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 660 VAL 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 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 102 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 644 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 847 LEU Chi-restraints excluded: chain D residue 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1064 ILE Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 185 PHE Chi-restraints excluded: chain I residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 251 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.0050 chunk 277 optimal weight: 10.0000 chunk 350 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 370 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** 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 = 0.3825 r_free = 0.3825 target = 0.092076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065731 restraints weight = 116625.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.067644 restraints weight = 58130.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.068877 restraints weight = 37752.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069641 restraints weight = 28898.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070101 restraints weight = 24599.637| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32336 Z= 0.126 Angle : 0.626 11.583 44489 Z= 0.330 Chirality : 0.044 0.306 5076 Planarity : 0.004 0.053 5274 Dihedral : 20.083 173.093 5663 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.07 % Allowed : 28.59 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3618 helix: 0.98 (0.14), residues: 1392 sheet: -0.70 (0.28), residues: 357 loop : -1.10 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG M 204 TYR 0.034 0.001 TYR K 220 PHE 0.043 0.002 PHE K 185 TRP 0.029 0.001 TRP M 166 HIS 0.007 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (32329) covalent geometry : angle 0.62587 / 0.33 (44483) hydrogen bonds : bond 0.04373 / 3.11 ( 1368) hydrogen bonds : angle 4.56993 / 3.20 ( 3787) metal coordination : bond 0.00304 / 0.15 ( 7) metal coordination : angle 2.23781 / 0.73 ( 6) *********************** 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 368 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 275 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8726 (m-30) cc_final: 0.8388 (p0) REVERT: B 168 TYR cc_start: 0.8859 (m-80) cc_final: 0.8260 (m-80) REVERT: C 154 MET cc_start: 0.9218 (mmm) cc_final: 0.8911 (tpp) REVERT: C 396 MET cc_start: 0.8674 (tmm) cc_final: 0.8309 (tmm) REVERT: C 440 MET cc_start: 0.8980 (tmm) cc_final: 0.8406 (tmm) REVERT: C 818 GLU cc_start: 0.7463 (tp30) cc_final: 0.6875 (tm-30) REVERT: C 837 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8345 (mp) REVERT: C 1063 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7781 (t80) REVERT: D 203 ARG cc_start: 0.8500 (ttm170) cc_final: 0.8126 (mpt180) REVERT: D 323 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8362 (mm-30) REVERT: D 376 GLU cc_start: 0.8701 (tp30) cc_final: 0.8255 (tp30) REVERT: D 379 ASP cc_start: 0.8395 (p0) cc_final: 0.7964 (p0) REVERT: D 513 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8100 (tm-30) REVERT: D 820 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7394 (ppp) REVERT: F 282 MET cc_start: 0.9039 (ttm) cc_final: 0.8737 (mmp) REVERT: F 485 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: F 502 ARG cc_start: 0.8101 (mmp-170) cc_final: 0.7461 (tpp-160) REVERT: J 197 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8508 (ttmt) REVERT: J 201 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8171 (t70) REVERT: J 244 ARG cc_start: 0.4895 (mmt180) cc_final: 0.4675 (mmt180) REVERT: M 153 PHE cc_start: 0.6044 (t80) cc_final: 0.5272 (t80) REVERT: M 244 ARG cc_start: 0.6418 (mmp80) cc_final: 0.5995 (mmm160) outliers start: 93 outliers final: 75 residues processed: 346 average time/residue: 0.1984 time to fit residues: 113.1515 Evaluate side-chains 342 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 262 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET 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 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 VAL 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 224 VAL Chi-restraints excluded: chain C residue 244 THR 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 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 691 ASP 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 C residue 1073 CYS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 101 VAL 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 441 CYS Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 580 ASP 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 733 MET Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 796 ASP 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 957 ILE Chi-restraints excluded: chain D residue 982 SER 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 446 VAL Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 215 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 0.0010 chunk 23 optimal weight: 9.9990 chunk 341 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 243 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 343 optimal weight: 3.9990 overall best weight: 1.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.091878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.065470 restraints weight = 116341.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.067370 restraints weight = 57644.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068599 restraints weight = 37189.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.069400 restraints weight = 28394.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.069822 restraints weight = 24051.193| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32336 Z= 0.134 Angle : 0.633 9.458 44489 Z= 0.333 Chirality : 0.044 0.303 5076 Planarity : 0.004 0.063 5274 Dihedral : 20.055 173.031 5663 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.94 % Allowed : 29.02 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.14), residues: 3618 helix: 0.97 (0.14), residues: 1393 sheet: -0.70 (0.28), residues: 357 loop : -1.09 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 183 TYR 0.050 0.001 TYR K 220 PHE 0.024 0.001 PHE I 185 TRP 0.033 0.001 TRP M 166 HIS 0.007 0.001 HIS K 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (32329) covalent geometry : angle 0.63197 / 0.33 (44483) hydrogen bonds : bond 0.04332 / 3.07 ( 1368) hydrogen bonds : angle 4.54804 / 3.18 ( 3787) metal coordination : bond 0.00401 / 0.19 ( 7) metal coordination : angle 2.43353 / 0.78 ( 6) *********************** 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 357 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 268 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8792 (m-30) cc_final: 0.8390 (p0) REVERT: B 168 TYR cc_start: 0.8870 (m-80) cc_final: 0.8255 (m-80) REVERT: C 154 MET cc_start: 0.9297 (mmm) cc_final: 0.9046 (tpp) REVERT: C 396 MET cc_start: 0.8683 (tmm) cc_final: 0.8315 (tmm) REVERT: C 420 ILE cc_start: 0.9131 (pt) cc_final: 0.8792 (mm) REVERT: C 440 MET cc_start: 0.8987 (tmm) cc_final: 0.8412 (tmm) REVERT: C 611 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8319 (mtm) REVERT: C 771 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7439 (ttm-80) REVERT: C 818 GLU cc_start: 0.7477 (tp30) cc_final: 0.6920 (tm-30) REVERT: C 837 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8361 (mp) REVERT: C 841 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.7422 (m90) REVERT: C 1063 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7727 (t80) REVERT: D 203 ARG cc_start: 0.8444 (ttm170) cc_final: 0.8072 (mpt180) REVERT: D 323 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8367 (mm-30) REVERT: D 376 GLU cc_start: 0.8704 (tp30) cc_final: 0.8255 (tp30) REVERT: D 379 ASP cc_start: 0.8404 (p0) cc_final: 0.7940 (p0) REVERT: D 513 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 820 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7367 (ppp) REVERT: F 263 MET cc_start: 0.8814 (tmm) cc_final: 0.8558 (mtt) REVERT: F 281 MET cc_start: 0.8639 (mmm) cc_final: 0.8422 (mmm) REVERT: F 485 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: F 502 ARG cc_start: 0.8123 (mmp-170) cc_final: 0.7479 (tpp-160) REVERT: J 182 LEU cc_start: 0.9121 (tp) cc_final: 0.8838 (tp) REVERT: J 201 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8169 (t70) outliers start: 89 outliers final: 71 residues processed: 333 average time/residue: 0.1916 time to fit residues: 105.5268 Evaluate side-chains 336 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 257 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET 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 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 VAL 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 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 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 820 LEU 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 33 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 441 CYS Chi-restraints excluded: chain D residue 580 ASP 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 737 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 796 ASP 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 957 ILE Chi-restraints excluded: chain D residue 982 SER 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 446 VAL Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 227 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 319 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 257 optimal weight: 0.0670 chunk 144 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 HIS ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN K 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.091543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065262 restraints weight = 116039.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.067132 restraints weight = 57463.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068348 restraints weight = 37116.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069034 restraints weight = 28429.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.069571 restraints weight = 24398.553| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32336 Z= 0.142 Angle : 0.642 12.659 44489 Z= 0.337 Chirality : 0.044 0.301 5076 Planarity : 0.004 0.065 5274 Dihedral : 20.041 173.155 5663 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.77 % Allowed : 29.12 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3618 helix: 0.96 (0.14), residues: 1394 sheet: -0.65 (0.29), residues: 356 loop : -1.07 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 183 TYR 0.048 0.001 TYR K 220 PHE 0.051 0.002 PHE K 185 TRP 0.040 0.001 TRP M 166 HIS 0.009 0.001 HIS K 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (32329) covalent geometry : angle 0.64103 / 0.34 (44483) hydrogen bonds : bond 0.04354 / 3.09 ( 1368) hydrogen bonds : angle 4.52312 / 3.16 ( 3787) metal coordination : bond 0.00476 / 0.23 ( 7) metal coordination : angle 2.47689 / 0.80 ( 6) ********************** 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 351 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 267 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8793 (m-30) cc_final: 0.8397 (p0) REVERT: B 168 TYR cc_start: 0.8882 (m-80) cc_final: 0.8162 (m-80) REVERT: C 154 MET cc_start: 0.9318 (mmm) cc_final: 0.9049 (tpp) REVERT: C 396 MET cc_start: 0.8695 (tmm) cc_final: 0.8322 (tmm) REVERT: C 420 ILE cc_start: 0.9127 (pt) cc_final: 0.8651 (mm) REVERT: C 440 MET cc_start: 0.8994 (tmm) cc_final: 0.8423 (tmm) REVERT: C 611 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8317 (mtm) REVERT: C 771 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7186 (ttt-90) REVERT: C 818 GLU cc_start: 0.7465 (tp30) cc_final: 0.6919 (tm-30) REVERT: C 837 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8656 (mp) REVERT: C 841 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7462 (m90) REVERT: C 1063 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7762 (t80) REVERT: C 1127 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7903 (mp0) REVERT: D 203 ARG cc_start: 0.8440 (ttm170) cc_final: 0.8070 (mpt180) REVERT: D 323 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8327 (mm-30) REVERT: D 376 GLU cc_start: 0.8688 (tp30) cc_final: 0.8228 (tp30) REVERT: D 379 ASP cc_start: 0.8394 (p0) cc_final: 0.7838 (p0) REVERT: D 513 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 820 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7366 (ppp) REVERT: F 263 MET cc_start: 0.8813 (tmm) cc_final: 0.8562 (mtt) REVERT: F 281 MET cc_start: 0.8656 (mmm) cc_final: 0.8431 (mmm) REVERT: F 485 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: F 502 ARG cc_start: 0.8058 (mmp-170) cc_final: 0.7405 (tpp-160) REVERT: J 197 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8593 (ttmt) REVERT: J 201 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.8206 (t70) REVERT: J 223 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8217 (mpt180) outliers start: 84 outliers final: 71 residues processed: 329 average time/residue: 0.1829 time to fit residues: 100.8663 Evaluate side-chains 340 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 261 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 95 MET 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 66 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 VAL 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 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 531 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 591 THR Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 691 ASP Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 820 LEU 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 D residue 2 LEU Chi-restraints excluded: chain D residue 33 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 441 CYS Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain D residue 756 VAL Chi-restraints excluded: chain D residue 796 ASP 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 862 ASP Chi-restraints excluded: chain D residue 957 ILE Chi-restraints excluded: chain D residue 982 SER Chi-restraints excluded: chain D residue 1064 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 446 VAL Chi-restraints excluded: chain F residue 485 GLN Chi-restraints excluded: chain F residue 492 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 514 LEU Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 163 HIS Chi-restraints excluded: chain K residue 165 VAL Chi-restraints excluded: chain K residue 199 LEU Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 6 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 83 optimal weight: 0.0030 chunk 196 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 311 optimal weight: 0.4980 chunk 195 optimal weight: 8.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 ASN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 HIS D 854 HIS ** F 325 ASN ** 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 = 0.3834 r_free = 0.3834 target = 0.093033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067301 restraints weight = 115547.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069172 restraints weight = 57028.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.070397 restraints weight = 36589.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071075 restraints weight = 27783.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.071631 restraints weight = 23789.698| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32336 Z= 0.125 Angle : 0.631 12.342 44489 Z= 0.331 Chirality : 0.044 0.301 5076 Planarity : 0.004 0.053 5274 Dihedral : 20.015 174.375 5663 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.57 % Allowed : 29.49 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.14), residues: 3618 helix: 0.99 (0.14), residues: 1391 sheet: -0.58 (0.29), residues: 355 loop : -1.04 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 173 TYR 0.048 0.001 TYR K 220 PHE 0.029 0.001 PHE K 179 TRP 0.041 0.001 TRP M 166 HIS 0.006 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (32329) covalent geometry : angle 0.63037 / 0.33 (44483) hydrogen bonds : bond 0.04211 / 2.99 ( 1368) hydrogen bonds : angle 4.46469 / 3.12 ( 3787) metal coordination : bond 0.00332 / 0.16 ( 7) metal coordination : angle 2.10718 / 0.70 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6973.93 seconds wall clock time: 120 minutes 33.99 seconds (7233.99 seconds total)