Starting phenix.real_space_refine on Sun Jan 19 00:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r8r_19008/01_2025/8r8r_19008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r8r_19008/01_2025/8r8r_19008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r8r_19008/01_2025/8r8r_19008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r8r_19008/01_2025/8r8r_19008.map" model { file = "/net/cci-nas-00/data/ceres_data/8r8r_19008/01_2025/8r8r_19008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r8r_19008/01_2025/8r8r_19008.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 6 5.49 5 S 83 5.16 5 C 8382 2.51 5 N 2285 2.21 5 O 2330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 13089 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9069 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 65, 'TRANS': 1122} Chain breaks: 10 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 30, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 241 Chain: "B" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2959 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 15, 'TRANS': 355} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 826 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 13} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 130 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 1} Link IDs: {'rna2p': 5} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12292 SG CYS C 41 29.823 90.056 100.958 1.00 54.94 S ATOM 12345 SG CYS C 49 26.930 90.899 103.204 1.00 72.06 S ATOM 12377 SG CYS C 55 28.176 87.336 103.145 1.00 66.85 S ATOM 12475 SG CYS C 68 46.200 82.355 112.414 1.00 75.39 S ATOM 12545 SG CYS C 76 42.561 81.175 112.465 1.00 72.25 S ATOM 12590 SG CYS C 82 43.421 84.849 113.239 1.00 81.25 S ATOM 12703 SG CYS C 96 62.993 80.180 115.009 1.00 82.54 S ATOM 12783 SG CYS C 105 65.197 77.251 113.867 1.00 94.85 S ATOM 12813 SG CYS C 110 62.544 78.676 111.535 1.00 82.21 S Time building chain proxies: 7.77, per 1000 atoms: 0.59 Number of scatterers: 13089 At special positions: 0 Unit cell: (87.6736, 107.251, 138.746, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 83 16.00 P 6 15.00 O 2330 8.00 N 2285 7.00 C 8382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" NE2 HIS C 86 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 68 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 82 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 76 " pdb=" ZN C 303 " pdb="ZN ZN C 303 " - pdb=" NE2 HIS C 114 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 110 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 96 " pdb="ZN ZN C 303 " - pdb=" SG CYS C 105 " Number of angles added : 9 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 29 sheets defined 10.6% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.877A pdb=" N VAL A 231 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ALA A 232 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 4.119A pdb=" N THR A 304 " --> pdb=" O ASN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.507A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 3.674A pdb=" N PHE A1291 " --> pdb=" O LYS A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.874A pdb=" N MET A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 3.573A pdb=" N ARG A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1405 Processing helix chain 'A' and resid 1405 through 1410 removed outlier: 3.705A pdb=" N TYR A1409 " --> pdb=" O ASN A1405 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1410 " --> pdb=" O ARG A1406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1405 through 1410' Processing helix chain 'A' and resid 1411 through 1422 removed outlier: 3.711A pdb=" N ILE A1422 " --> pdb=" O LEU A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1440 removed outlier: 3.805A pdb=" N THR A1436 " --> pdb=" O ASP A1432 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.546A pdb=" N VAL B 106 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 21 removed outlier: 3.564A pdb=" N ILE C 17 " --> pdb=" O PHE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.805A pdb=" N CYS C 55 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 3.553A pdb=" N ARG C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.502A pdb=" N LYS C 92 " --> pdb=" O ASP C 89 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 93 " --> pdb=" O MET C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 96 through 102 Processing sheet with id=AA1, first strand: chain 'A' and resid 1308 through 1315 removed outlier: 4.306A pdb=" N THR A1310 " --> pdb=" O ALA A1339 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A1339 " --> pdb=" O THR A1310 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 24 removed outlier: 4.642A pdb=" N PHE A 22 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N GLU A 27 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N ARG A 28 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 43 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 84 removed outlier: 3.857A pdb=" N SER A 80 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 114 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.631A pdb=" N TYR A 189 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.646A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER A 260 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER A 244 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 254 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.749A pdb=" N PHE A 281 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 279 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329 removed outlier: 7.476A pdb=" N ILE A 344 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS A 364 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 346 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE A 362 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.501A pdb=" N SER A 373 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 391 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A 468 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 393 " --> pdb=" O CYS A 466 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 528 removed outlier: 6.752A pdb=" N ILE A 998 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 526 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 996 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.921A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY A 573 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 592 " --> pdb=" O ARG D 742 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.581A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS A 636 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 651 removed outlier: 3.557A pdb=" N GLN A 648 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703 removed outlier: 3.923A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 796 " --> pdb=" O PHE A 806 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 806 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN A 798 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 804 " --> pdb=" O GLN A 798 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.560A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 876 " --> pdb=" O PRO A 861 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.653A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER A 941 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 955 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1021 through 1028 removed outlier: 6.695A pdb=" N ALA A1037 " --> pdb=" O HIS A1023 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL A1025 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A1035 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR A1027 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A1033 " --> pdb=" O TYR A1027 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A1078 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALA A1090 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N SER A1080 " --> pdb=" O PRO A1088 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1046 through 1049 Processing sheet with id=AC1, first strand: chain 'A' and resid 1098 through 1109 removed outlier: 6.593A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A1107 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS A1118 " --> pdb=" O SER A1107 " (cutoff:3.500A) removed outlier: 20.228A pdb=" N LEU A1117 " --> pdb=" O GLU A1146 " (cutoff:3.500A) removed outlier: 15.865A pdb=" N GLU A1146 " --> pdb=" O LEU A1117 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N GLY A1119 " --> pdb=" O VAL A1144 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A1144 " --> pdb=" O GLY A1119 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 4.010A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1212 through 1218 removed outlier: 3.983A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1247 " --> pdb=" O LEU A1233 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG A1235 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A1245 " --> pdb=" O ARG A1235 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLN A1237 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A1243 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1255 through 1262 removed outlier: 4.610A pdb=" N SER A1257 " --> pdb=" O SER A1272 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A1273 " --> pdb=" O ASN A1277 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 109 through 114 removed outlier: 5.583A pdb=" N PHE B 110 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR B 403 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG B 112 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE B 389 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TRP B 383 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS B 391 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU B 381 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY B 393 " --> pdb=" O TRP B 379 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 122 through 127 removed outlier: 4.438A pdb=" N GLU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR B 155 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASN B 147 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 153 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.541A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 205 through 210 removed outlier: 4.187A pdb=" N GLU B 207 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 238 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASP B 230 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU B 236 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.889A pdb=" N ILE B 270 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 283 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE B 272 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 291 through 296 removed outlier: 3.551A pdb=" N GLU B 293 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 325 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.725A pdb=" N ALA B 336 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 368 " --> pdb=" O PHE B 358 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4175 1.34 - 1.45: 1996 1.45 - 1.57: 7113 1.57 - 1.69: 11 1.69 - 1.81: 129 Bond restraints: 13424 Sorted by residual: bond pdb=" CA ASP B 214 " pdb=" CB ASP B 214 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.70e-02 3.46e+03 7.99e-01 bond pdb=" C ASP A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.40e-01 bond pdb=" C VAL A 647 " pdb=" O VAL A 647 " ideal model delta sigma weight residual 1.245 1.235 0.010 1.41e-02 5.03e+03 4.92e-01 bond pdb=" N PRO A 10 " pdb=" CA PRO A 10 " ideal model delta sigma weight residual 1.459 1.469 -0.009 1.40e-02 5.10e+03 4.29e-01 bond pdb=" N VAL A 271 " pdb=" CA VAL A 271 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.24e-01 ... (remaining 13419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 17543 1.08 - 2.17: 570 2.17 - 3.25: 142 3.25 - 4.34: 24 4.34 - 5.42: 9 Bond angle restraints: 18288 Sorted by residual: angle pdb=" C THR B 213 " pdb=" N ASP B 214 " pdb=" CA ASP B 214 " ideal model delta sigma weight residual 122.46 127.44 -4.98 1.41e+00 5.03e-01 1.25e+01 angle pdb=" N VAL A 647 " pdb=" CA VAL A 647 " pdb=" C VAL A 647 " ideal model delta sigma weight residual 113.71 111.15 2.56 9.50e-01 1.11e+00 7.26e+00 angle pdb=" C HIS A1373 " pdb=" N ALA A1374 " pdb=" CA ALA A1374 " ideal model delta sigma weight residual 121.54 126.44 -4.90 1.91e+00 2.74e-01 6.57e+00 angle pdb=" N ILE A 320 " pdb=" CA ILE A 320 " pdb=" C ILE A 320 " ideal model delta sigma weight residual 108.53 111.44 -2.91 1.22e+00 6.72e-01 5.67e+00 angle pdb=" CA VAL A 647 " pdb=" C VAL A 647 " pdb=" N GLN A 648 " ideal model delta sigma weight residual 119.87 117.35 2.52 1.34e+00 5.57e-01 3.52e+00 ... (remaining 18283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 7195 16.54 - 33.08: 561 33.08 - 49.62: 112 49.62 - 66.16: 22 66.16 - 82.70: 13 Dihedral angle restraints: 7903 sinusoidal: 3037 harmonic: 4866 Sorted by residual: dihedral pdb=" CA PRO A 272 " pdb=" C PRO A 272 " pdb=" N LYS A 273 " pdb=" CA LYS A 273 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ILE A 472 " pdb=" C ILE A 472 " pdb=" N GLY A 473 " pdb=" CA GLY A 473 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 91 " pdb=" CB ASP B 91 " pdb=" CG ASP B 91 " pdb=" OD1 ASP B 91 " ideal model delta sinusoidal sigma weight residual -30.00 -87.77 57.77 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 7900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1276 0.032 - 0.064: 521 0.064 - 0.096: 142 0.096 - 0.128: 137 0.128 - 0.160: 7 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA ASP B 214 " pdb=" N ASP B 214 " pdb=" C ASP B 214 " pdb=" CB ASP B 214 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA ILE A 998 " pdb=" N ILE A 998 " pdb=" C ILE A 998 " pdb=" CB ILE A 998 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA PRO B 129 " pdb=" N PRO B 129 " pdb=" C PRO B 129 " pdb=" CB PRO B 129 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 2080 not shown) Planarity restraints: 2304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 384 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 385 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 271 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 272 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 94 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 95 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.022 5.00e-02 4.00e+02 ... (remaining 2301 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3052 2.80 - 3.32: 9710 3.32 - 3.85: 19775 3.85 - 4.37: 24480 4.37 - 4.90: 43943 Nonbonded interactions: 100960 Sorted by model distance: nonbonded pdb=" OH TYR A1066 " pdb=" OD2 ASP B 85 " model vdw 2.275 3.040 nonbonded pdb=" OD2 ASP A 596 " pdb=" ND2 ASN D 744 " model vdw 2.364 3.120 nonbonded pdb=" OE2 GLU A 222 " pdb=" OG1 THR A 237 " model vdw 2.367 3.040 nonbonded pdb=" O ASP A 46 " pdb=" NH1 ARG A 857 " model vdw 2.385 3.120 nonbonded pdb=" OG SER A 239 " pdb=" O LEU A 258 " model vdw 2.397 3.040 ... (remaining 100955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.450 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13424 Z= 0.156 Angle : 0.500 5.420 18288 Z= 0.267 Chirality : 0.044 0.160 2083 Planarity : 0.004 0.044 2304 Dihedral : 12.996 82.695 4759 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1653 helix: -0.34 (0.53), residues: 103 sheet: 0.88 (0.21), residues: 606 loop : -0.90 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1312 HIS 0.008 0.001 HIS B 397 PHE 0.019 0.001 PHE A 901 TYR 0.008 0.001 TYR A1066 ARG 0.003 0.000 ARG A1235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 794 MET cc_start: 0.7946 (tmm) cc_final: 0.7720 (ttm) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 1.3567 time to fit residues: 144.6845 Evaluate side-chains 76 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.045767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.034950 restraints weight = 44073.241| |-----------------------------------------------------------------------------| r_work (start): 0.2358 rms_B_bonded: 3.11 r_work: 0.2233 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13424 Z= 0.338 Angle : 0.560 7.297 18288 Z= 0.301 Chirality : 0.045 0.149 2083 Planarity : 0.004 0.047 2304 Dihedral : 5.446 58.296 1879 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.66 % Allowed : 5.39 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1653 helix: 0.22 (0.54), residues: 102 sheet: 0.89 (0.20), residues: 625 loop : -0.90 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1312 HIS 0.003 0.001 HIS A1334 PHE 0.013 0.001 PHE A1160 TYR 0.007 0.001 TYR A 989 ARG 0.006 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8567 (ttm) cc_final: 0.7916 (tpp) REVERT: C 16 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8426 (mt-10) REVERT: C 20 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8586 (tm-30) REVERT: C 21 GLN cc_start: 0.9429 (mm110) cc_final: 0.9139 (mm-40) REVERT: C 89 ASP cc_start: 0.8725 (t0) cc_final: 0.8368 (t0) REVERT: C 101 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8752 (ttpp) REVERT: C 107 ASN cc_start: 0.8538 (t0) cc_final: 0.8098 (t0) REVERT: D 737 ASN cc_start: 0.8759 (t0) cc_final: 0.8031 (m-40) outliers start: 9 outliers final: 4 residues processed: 84 average time/residue: 1.4367 time to fit residues: 132.8945 Evaluate side-chains 79 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 36 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 128 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 120 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.047524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.036750 restraints weight = 44454.411| |-----------------------------------------------------------------------------| r_work (start): 0.2419 rms_B_bonded: 3.17 r_work: 0.2298 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13424 Z= 0.117 Angle : 0.465 9.596 18288 Z= 0.245 Chirality : 0.043 0.153 2083 Planarity : 0.004 0.047 2304 Dihedral : 5.073 57.668 1879 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.74 % Allowed : 6.35 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1653 helix: 0.51 (0.55), residues: 101 sheet: 0.95 (0.20), residues: 630 loop : -0.79 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1312 HIS 0.002 0.000 HIS B 374 PHE 0.010 0.001 PHE B 217 TYR 0.008 0.001 TYR A 989 ARG 0.003 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8525 (ttm) cc_final: 0.7884 (tpp) REVERT: B 48 MET cc_start: 0.8204 (tpp) cc_final: 0.7941 (tpp) REVERT: C 16 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8471 (mt-10) REVERT: C 104 GLU cc_start: 0.8861 (pm20) cc_final: 0.8655 (pm20) REVERT: C 107 ASN cc_start: 0.8637 (t0) cc_final: 0.8177 (t0) REVERT: D 737 ASN cc_start: 0.8799 (t0) cc_final: 0.8078 (m-40) outliers start: 10 outliers final: 2 residues processed: 81 average time/residue: 1.3625 time to fit residues: 121.5907 Evaluate side-chains 77 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain C residue 36 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 136 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.044412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.033640 restraints weight = 44817.368| |-----------------------------------------------------------------------------| r_work (start): 0.2324 rms_B_bonded: 3.15 r_work: 0.2200 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13424 Z= 0.393 Angle : 0.562 8.489 18288 Z= 0.298 Chirality : 0.045 0.144 2083 Planarity : 0.004 0.046 2304 Dihedral : 5.395 57.614 1879 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.89 % Allowed : 7.31 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1653 helix: 0.46 (0.55), residues: 108 sheet: 0.90 (0.20), residues: 625 loop : -0.94 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 383 HIS 0.004 0.001 HIS B 310 PHE 0.015 0.001 PHE A1160 TYR 0.008 0.001 TYR A 39 ARG 0.002 0.000 ARG A 958 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 593 MET cc_start: 0.8876 (mtp) cc_final: 0.8480 (mtp) REVERT: A 1050 MET cc_start: 0.8625 (ttm) cc_final: 0.8002 (tpp) REVERT: C 16 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8455 (mt-10) REVERT: C 20 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8560 (tm-30) REVERT: C 21 GLN cc_start: 0.9417 (mm-40) cc_final: 0.9150 (mm-40) REVERT: C 107 ASN cc_start: 0.8781 (t0) cc_final: 0.8468 (t0) REVERT: D 737 ASN cc_start: 0.8860 (t0) cc_final: 0.8127 (m-40) outliers start: 12 outliers final: 4 residues processed: 81 average time/residue: 1.4987 time to fit residues: 134.1142 Evaluate side-chains 77 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 36 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 47 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.045270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.034451 restraints weight = 45168.978| |-----------------------------------------------------------------------------| r_work (start): 0.2354 rms_B_bonded: 3.19 r_work: 0.2229 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13424 Z= 0.216 Angle : 0.491 8.896 18288 Z= 0.261 Chirality : 0.043 0.143 2083 Planarity : 0.004 0.047 2304 Dihedral : 5.222 57.589 1879 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.59 % Allowed : 8.71 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1653 helix: 0.54 (0.55), residues: 108 sheet: 0.95 (0.20), residues: 626 loop : -0.91 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1312 HIS 0.002 0.001 HIS B 374 PHE 0.009 0.001 PHE B 347 TYR 0.008 0.001 TYR A 989 ARG 0.001 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 593 MET cc_start: 0.8842 (mtp) cc_final: 0.8461 (mtp) REVERT: A 1050 MET cc_start: 0.8598 (ttm) cc_final: 0.8022 (tpp) REVERT: C 16 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8445 (mt-10) REVERT: C 107 ASN cc_start: 0.8815 (t0) cc_final: 0.8461 (t0) REVERT: D 737 ASN cc_start: 0.8860 (t0) cc_final: 0.8112 (m-40) outliers start: 8 outliers final: 3 residues processed: 77 average time/residue: 1.4283 time to fit residues: 120.6234 Evaluate side-chains 77 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain C residue 36 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 122 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.044095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.033309 restraints weight = 46026.658| |-----------------------------------------------------------------------------| r_work (start): 0.2313 rms_B_bonded: 3.19 r_work: 0.2187 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13424 Z= 0.384 Angle : 0.563 11.543 18288 Z= 0.296 Chirality : 0.045 0.144 2083 Planarity : 0.004 0.046 2304 Dihedral : 5.394 57.597 1879 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.66 % Allowed : 9.89 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.20), residues: 1653 helix: 0.58 (0.55), residues: 108 sheet: 0.91 (0.20), residues: 621 loop : -1.00 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 383 HIS 0.004 0.001 HIS B 310 PHE 0.012 0.001 PHE A1160 TYR 0.008 0.001 TYR A 797 ARG 0.002 0.000 ARG A 958 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.571 Fit side-chains REVERT: A 593 MET cc_start: 0.8874 (mtp) cc_final: 0.8494 (mtp) REVERT: A 1050 MET cc_start: 0.8614 (ttm) cc_final: 0.8049 (tpp) REVERT: C 16 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8532 (mt-10) REVERT: C 20 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 21 GLN cc_start: 0.9423 (mm-40) cc_final: 0.9212 (mm-40) REVERT: C 89 ASP cc_start: 0.9061 (t0) cc_final: 0.8468 (t0) REVERT: C 107 ASN cc_start: 0.8866 (t0) cc_final: 0.8509 (t0) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 1.4006 time to fit residues: 121.2377 Evaluate side-chains 80 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 36 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 140 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.045199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2370 r_free = 0.2370 target = 0.034433 restraints weight = 45465.081| |-----------------------------------------------------------------------------| r_work (start): 0.2352 rms_B_bonded: 3.19 r_work: 0.2228 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13424 Z= 0.196 Angle : 0.494 9.333 18288 Z= 0.261 Chirality : 0.043 0.143 2083 Planarity : 0.004 0.048 2304 Dihedral : 5.188 57.593 1879 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.44 % Allowed : 10.85 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1653 helix: 0.67 (0.55), residues: 107 sheet: 0.85 (0.20), residues: 634 loop : -0.89 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1312 HIS 0.002 0.000 HIS B 397 PHE 0.010 0.001 PHE B 217 TYR 0.009 0.001 TYR A 989 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 1.647 Fit side-chains REVERT: A 593 MET cc_start: 0.8845 (mtp) cc_final: 0.8456 (mtp) REVERT: A 667 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9240 (ttp) REVERT: A 1050 MET cc_start: 0.8576 (ttm) cc_final: 0.8032 (tpp) REVERT: C 16 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8468 (mt-10) REVERT: C 20 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8566 (tm-30) REVERT: C 21 GLN cc_start: 0.9440 (mm-40) cc_final: 0.9219 (mm-40) REVERT: C 89 ASP cc_start: 0.9005 (t0) cc_final: 0.8405 (t0) REVERT: C 107 ASN cc_start: 0.8877 (t0) cc_final: 0.8515 (t0) REVERT: D 737 ASN cc_start: 0.8626 (t0) cc_final: 0.7837 (m-40) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 1.3983 time to fit residues: 119.7986 Evaluate side-chains 79 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 667 MET Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain B residue 249 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 96 optimal weight: 0.0980 chunk 113 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.046443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.035713 restraints weight = 45454.341| |-----------------------------------------------------------------------------| r_work (start): 0.2400 rms_B_bonded: 3.22 r_work: 0.2277 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13424 Z= 0.135 Angle : 0.475 10.937 18288 Z= 0.246 Chirality : 0.042 0.148 2083 Planarity : 0.004 0.050 2304 Dihedral : 4.921 57.616 1879 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.15 % Allowed : 11.66 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1653 helix: 1.05 (0.56), residues: 101 sheet: 0.93 (0.20), residues: 641 loop : -0.73 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1312 HIS 0.003 0.000 HIS B 397 PHE 0.011 0.001 PHE B 217 TYR 0.009 0.001 TYR A 989 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 1.680 Fit side-chains REVERT: A 593 MET cc_start: 0.8812 (mtp) cc_final: 0.8450 (mtp) REVERT: A 1050 MET cc_start: 0.8543 (ttm) cc_final: 0.8023 (tpp) REVERT: C 16 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8531 (mt-10) REVERT: C 101 LYS cc_start: 0.9214 (ttmm) cc_final: 0.8902 (ttpp) REVERT: C 107 ASN cc_start: 0.8880 (t0) cc_final: 0.8492 (t0) outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 1.4542 time to fit residues: 124.7745 Evaluate side-chains 76 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 3 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 737 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.043220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.032502 restraints weight = 46037.199| |-----------------------------------------------------------------------------| r_work (start): 0.2294 rms_B_bonded: 3.14 r_work: 0.2167 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 13424 Z= 0.608 Angle : 0.663 10.139 18288 Z= 0.347 Chirality : 0.048 0.172 2083 Planarity : 0.004 0.046 2304 Dihedral : 5.523 57.624 1879 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.81 % Allowed : 11.29 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1653 helix: 0.34 (0.54), residues: 114 sheet: 0.82 (0.20), residues: 627 loop : -0.96 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 383 HIS 0.006 0.001 HIS B 310 PHE 0.017 0.002 PHE A 975 TYR 0.010 0.001 TYR A1066 ARG 0.003 0.000 ARG A 958 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.286 Fit side-chains REVERT: A 593 MET cc_start: 0.8883 (mtp) cc_final: 0.8508 (mtp) REVERT: A 1050 MET cc_start: 0.8597 (ttm) cc_final: 0.8065 (tpp) REVERT: C 107 ASN cc_start: 0.9004 (t0) cc_final: 0.8654 (t0) outliers start: 11 outliers final: 4 residues processed: 81 average time/residue: 1.3876 time to fit residues: 123.2127 Evaluate side-chains 78 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 1314 THR Chi-restraints excluded: chain B residue 249 CYS Chi-restraints excluded: chain C residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 144 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 159 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 74 optimal weight: 0.0000 chunk 127 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 737 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.045585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.034942 restraints weight = 45124.848| |-----------------------------------------------------------------------------| r_work (start): 0.2373 rms_B_bonded: 3.17 r_work: 0.2247 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13424 Z= 0.135 Angle : 0.517 14.642 18288 Z= 0.268 Chirality : 0.044 0.298 2083 Planarity : 0.004 0.049 2304 Dihedral : 5.133 57.575 1879 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.30 % Allowed : 12.40 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1653 helix: 0.67 (0.55), residues: 107 sheet: 0.91 (0.20), residues: 629 loop : -0.83 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1312 HIS 0.005 0.000 HIS C 86 PHE 0.011 0.001 PHE C 84 TYR 0.010 0.001 TYR A 989 ARG 0.002 0.000 ARG B 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 1.586 Fit side-chains REVERT: A 593 MET cc_start: 0.8809 (mtp) cc_final: 0.8445 (mtp) REVERT: A 1050 MET cc_start: 0.8541 (ttm) cc_final: 0.8040 (tpp) REVERT: B 48 MET cc_start: 0.8703 (tpp) cc_final: 0.7770 (tpp) REVERT: C 34 ASP cc_start: 0.8660 (p0) cc_final: 0.8279 (p0) REVERT: C 36 SER cc_start: 0.9344 (t) cc_final: 0.9026 (p) REVERT: C 107 ASN cc_start: 0.8947 (t0) cc_final: 0.8583 (t0) outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 1.4613 time to fit residues: 121.6025 Evaluate side-chains 76 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 249 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 107 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 158 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 0.0060 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.046101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.035360 restraints weight = 45467.128| |-----------------------------------------------------------------------------| r_work (start): 0.2384 rms_B_bonded: 3.21 r_work: 0.2261 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13424 Z= 0.141 Angle : 0.486 11.056 18288 Z= 0.252 Chirality : 0.042 0.145 2083 Planarity : 0.004 0.049 2304 Dihedral : 4.947 57.620 1879 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.15 % Allowed : 12.47 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.20), residues: 1653 helix: 1.02 (0.56), residues: 101 sheet: 0.95 (0.20), residues: 637 loop : -0.71 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1312 HIS 0.003 0.000 HIS B 397 PHE 0.010 0.001 PHE B 217 TYR 0.009 0.001 TYR A 989 ARG 0.002 0.000 ARG B 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6318.00 seconds wall clock time: 112 minutes 45.66 seconds (6765.66 seconds total)