Starting phenix.real_space_refine on Sat Sep 12 08:43:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zgr_14712/09_2026/7zgr_14712.cif" } resolution = 2.6 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= 0.002 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 2 6.06 5 P 3 5.49 5 S 70 5.16 5 C 9254 2.51 5 N 2458 2.21 5 O 2718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14505 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1254, 9888 Classifications: {'peptide': 1254} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 52, 'TRANS': 1201} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 776 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 82} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 236 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 26} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3164 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 20, 'TRANS': 374} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Classifications: {'DNA': 1, 'RNAv2': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G:plan': 1, ' G:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 374 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10427 SG CYS B 67 38.515 29.711 29.046 1.00 87.90 S ATOM 10499 SG CYS B 75 37.646 29.839 32.779 1.00 82.52 S ATOM 10548 SG CYS B 81 37.523 26.453 30.900 1.00 94.34 S ATOM 10173 SG CYS B 34 54.982 11.644 41.276 1.00117.94 S ATOM 10261 SG CYS B 46 53.154 11.848 44.651 1.00123.05 S ATOM 10304 SG CYS B 52 56.473 13.752 44.151 1.00123.41 S Time building chain proxies: 3.19, per 1000 atoms: 0.22 Number of scatterers: 14505 At special positions: 0 Unit cell: (141.9, 117.975, 93.225, 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 2 29.99 S 70 16.00 P 3 15.00 O 2718 8.00 N 2458 7.00 C 9254 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: 1.16 Conformation dependent library (CDL) restraints added in 754.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 56 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 46 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 52 " Number of angles added : 6 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 28 sheets defined 11.3% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.674A pdb=" N THR A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N THR A 242 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 4.094A pdb=" N ASN A 700 " --> pdb=" O PRO A 696 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 696 through 701' Processing helix chain 'A' and resid 715 through 719 Processing helix chain 'A' and resid 841 through 846 removed outlier: 4.498A pdb=" N SER A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 removed outlier: 3.778A pdb=" N SER A1206 " --> pdb=" O GLU A1203 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1207 " --> pdb=" O PRO A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1203 through 1207' Processing helix chain 'A' and resid 1262 through 1280 Processing helix chain 'A' and resid 1287 through 1294 Processing helix chain 'A' and resid 1310 through 1318 removed outlier: 3.887A pdb=" N ARG A1315 " --> pdb=" O ASN A1311 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A1316 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS A1317 " --> pdb=" O ILE A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1329 Processing helix chain 'A' and resid 1334 through 1348 Processing helix chain 'A' and resid 1349 through 1355 removed outlier: 4.072A pdb=" N SER A1352 " --> pdb=" O SER A1349 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1355 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.786A pdb=" N CYS B 46 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.050A pdb=" N LEU B 51 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.653A pdb=" N ASN B 63 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.667A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.724A pdb=" N MET C 557 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE C 558 " --> pdb=" O PHE C 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 554 through 558' Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.740A pdb=" N ILE D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 72 through 80 removed outlier: 3.857A pdb=" N VAL D 77 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.557A pdb=" N GLU F 265 " --> pdb=" O GLN F 261 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1224 through 1231 removed outlier: 3.586A pdb=" N CYS A1226 " --> pdb=" O GLY A1249 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE A1244 " --> pdb=" O PRO A1260 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL A1255 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.679A pdb=" N LEU A 37 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU A 53 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 39 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 67 removed outlier: 7.832A pdb=" N SER A 74 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE A 90 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE A 85 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU A 102 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 87 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 125 Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 218 removed outlier: 6.751A pdb=" N LEU A 230 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 216 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA A 228 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A 218 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR A 226 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 248 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A 276 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 254 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR A 270 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN A 256 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N SER A 268 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN A 258 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE A 266 " --> pdb=" O GLN A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 281 through 286 removed outlier: 4.077A pdb=" N GLU A 298 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 310 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASP A 303 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 327 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.782A pdb=" N LEU A 363 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 388 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.471A pdb=" N GLY A 425 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 408 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 423 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG A 410 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ASP A 421 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 435 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 501 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 517 removed outlier: 4.180A pdb=" N SER A 513 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 525 through 526 Processing sheet with id=AB2, first strand: chain 'A' and resid 561 through 567 removed outlier: 5.834A pdb=" N ILE A 562 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 915 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 564 " --> pdb=" O VAL A 913 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 577 removed outlier: 3.739A pdb=" N GLN A 573 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 577 " --> pdb=" O TYR A 585 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR A 585 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 619 through 625 removed outlier: 6.763A pdb=" N VAL A 634 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 622 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE A 632 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET A 624 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG A 630 " --> pdb=" O MET A 624 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS A 638 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 658 through 663 removed outlier: 6.661A pdb=" N THR A 671 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A 661 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 669 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL A 663 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR A 667 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 712 removed outlier: 4.928A pdb=" N ILE A 741 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU A 797 " --> pdb=" O LYS A 813 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 851 through 854 Processing sheet with id=AB8, first strand: chain 'A' and resid 944 through 950 removed outlier: 5.968A pdb=" N LEU A 944 " --> pdb=" O CYS A 961 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS A 961 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS A 946 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 959 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER A 991 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP A1008 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 993 " --> pdb=" O LYS A1006 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A1006 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 995 " --> pdb=" O ILE A1004 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1013 through 1023 removed outlier: 5.240A pdb=" N VAL A1015 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A1041 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU A1034 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL A1059 " --> pdb=" O GLU A1034 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR A1051 " --> pdb=" O ASN A1042 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY A1052 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A1082 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE A1054 " --> pdb=" O GLN A1080 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLN A1080 " --> pdb=" O PHE A1054 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A1056 " --> pdb=" O ILE A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 7.021A pdb=" N VAL A1105 " --> pdb=" O PHE A1121 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE A1121 " --> pdb=" O VAL A1105 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A1107 " --> pdb=" O VAL A1119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1128 through 1134 removed outlier: 4.165A pdb=" N ASP A1130 " --> pdb=" O GLY A1141 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE A1147 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A1151 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N SER A1161 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP A1153 " --> pdb=" O MET A1159 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N MET A1159 " --> pdb=" O ASP A1153 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A1212 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A1164 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS A1214 " --> pdb=" O ARG A1164 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A1196 " --> pdb=" O CYS A1215 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A1217 " --> pdb=" O VAL A1194 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A1194 " --> pdb=" O SER A1217 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR A1184 " --> pdb=" O PHE A1176 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE A1176 " --> pdb=" O TYR A1184 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA A1186 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU A1174 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR A1188 " --> pdb=" O MET A1172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 83 through 88 removed outlier: 5.295A pdb=" N PHE D 84 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR D 378 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.340A pdb=" N ALA D 98 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 138 through 143 removed outlier: 4.143A pdb=" N THR D 140 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE D 161 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 180 through 185 removed outlier: 6.744A pdb=" N CYS D 195 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET D 183 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 193 " --> pdb=" O MET D 183 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE D 185 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS D 191 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 196 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG D 213 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN D 205 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLN D 211 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 222 through 227 removed outlier: 6.529A pdb=" N VAL D 243 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER D 256 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU D 245 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 264 through 269 removed outlier: 3.544A pdb=" N LYS D 266 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET D 299 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP D 290 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU D 297 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 307 through 312 removed outlier: 6.775A pdb=" N ALA D 323 " --> pdb=" O MET D 308 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU D 310 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR D 321 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TRP D 312 " --> pdb=" O MET D 319 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N MET D 319 " --> pdb=" O TRP D 312 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS D 324 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER D 328 " --> pdb=" O CYS D 324 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 209 through 210 removed outlier: 6.362A pdb=" N ARG F 209 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE F 241 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE F 247 " --> pdb=" O ILE F 222 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1119 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: 3.49 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4516 1.33 - 1.46: 2619 1.46 - 1.58: 7574 1.58 - 1.70: 6 1.70 - 1.82: 115 Bond restraints: 14830 Sorted by residual: bond pdb=" N ILE D 280 " pdb=" CA ILE D 280 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.22e-02 6.72e+03 8.37e+00 bond pdb=" N VAL D 264 " pdb=" CA VAL D 264 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.10e-02 8.26e+03 8.27e+00 bond pdb=" N VAL A1255 " pdb=" CA VAL A1255 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.17e-02 7.31e+03 7.97e+00 bond pdb=" N GLN A1250 " pdb=" CA GLN A1250 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.18e-02 7.18e+03 7.57e+00 bond pdb=" N VAL A 508 " pdb=" CA VAL A 508 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.05e+00 ... (remaining 14825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 19753 1.94 - 3.88: 322 3.88 - 5.83: 31 5.83 - 7.77: 3 7.77 - 9.71: 1 Bond angle restraints: 20110 Sorted by residual: angle pdb=" N ASP D 283 " pdb=" CA ASP D 283 " pdb=" C ASP D 283 " ideal model delta sigma weight residual 113.15 107.95 5.20 1.19e+00 7.06e-01 1.91e+01 angle pdb=" N LYS D 282 " pdb=" CA LYS D 282 " pdb=" C LYS D 282 " ideal model delta sigma weight residual 113.19 108.52 4.67 1.19e+00 7.06e-01 1.54e+01 angle pdb=" N ILE A 977 " pdb=" CA ILE A 977 " pdb=" C ILE A 977 " ideal model delta sigma weight residual 110.23 113.89 -3.66 1.04e+00 9.25e-01 1.24e+01 angle pdb=" N ILE A 571 " pdb=" CA ILE A 571 " pdb=" C ILE A 571 " ideal model delta sigma weight residual 111.62 108.98 2.64 7.90e-01 1.60e+00 1.11e+01 angle pdb=" N PHE D 418 " pdb=" CA PHE D 418 " pdb=" C PHE D 418 " ideal model delta sigma weight residual 114.64 109.71 4.93 1.52e+00 4.33e-01 1.05e+01 ... (remaining 20105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7991 17.61 - 35.22: 726 35.22 - 52.83: 175 52.83 - 70.44: 37 70.44 - 88.06: 15 Dihedral angle restraints: 8944 sinusoidal: 3610 harmonic: 5334 Sorted by residual: dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" C2' A E 2 " pdb=" C1' A E 2 " ideal model delta sinusoidal sigma weight residual 36.34 -35.01 71.35 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" C4' A E 1 " pdb=" C3' A E 1 " pdb=" C2' A E 1 " pdb=" C1' A E 1 " ideal model delta sinusoidal sigma weight residual 36.35 -34.88 71.22 1 3.10e+00 1.04e-01 6.77e+02 dihedral pdb=" O4' A E 2 " pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" C2' A E 2 " ideal model delta sinusoidal sigma weight residual -35.15 25.86 -61.00 1 4.00e+00 6.25e-02 3.09e+02 ... (remaining 8941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1833 0.056 - 0.112: 385 0.112 - 0.167: 44 0.167 - 0.223: 6 0.223 - 0.279: 5 Chirality restraints: 2273 Sorted by residual: chirality pdb=" C2' A E 1 " pdb=" C3' A E 1 " pdb=" O2' A E 1 " pdb=" C1' A E 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' A E 2 " pdb=" C3' A E 2 " pdb=" O2' A E 2 " pdb=" C1' A E 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE A 598 " pdb=" CA ILE A 598 " pdb=" CG1 ILE A 598 " pdb=" CG2 ILE A 598 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2270 not shown) Planarity restraints: 2561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 390 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO D 391 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 391 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 391 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1155 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A1156 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A1156 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1156 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 983 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 984 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " 0.021 5.00e-02 4.00e+02 ... (remaining 2558 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 809 2.73 - 3.27: 14155 3.27 - 3.81: 25170 3.81 - 4.36: 32424 4.36 - 4.90: 54501 Nonbonded interactions: 127059 Sorted by model distance: nonbonded pdb=" N GLU A1264 " pdb=" OE1 GLU A1264 " model vdw 2.181 3.120 nonbonded pdb=" N GLU A 697 " pdb=" OE1 GLU A 697 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR A1266 " pdb=" O PRO A1306 " model vdw 2.206 3.040 nonbonded pdb=" O ASP A 583 " pdb=" OG SER A 601 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS A 84 " pdb=" OE2 GLU A1291 " model vdw 2.252 3.120 ... (remaining 127054 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 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 : 0.003 0.072 14838 Z= 0.185 Angle : 0.572 9.712 20116 Z= 0.324 Chirality : 0.048 0.279 2273 Planarity : 0.004 0.063 2561 Dihedral : 14.884 88.056 5488 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 1.24 % Allowed : 12.66 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.19), residues: 1801 helix: 0.23 (0.50), residues: 120 sheet: 0.69 (0.22), residues: 561 loop : -1.01 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 688 TYR 0.011 0.001 TYR A 250 PHE 0.012 0.001 PHE A 625 TRP 0.009 0.001 TRP D 312 HIS 0.005 0.000 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.19 (14830) covalent geometry : angle 0.57228 / 0.32 (20110) hydrogen bonds : bond 0.22644 / 15.46 ( 431) hydrogen bonds : angle 8.67897 / 5.92 ( 1119) metal coordination : bond 0.00628 / 0.33 ( 8) metal coordination : angle 0.87965 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.664 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: D 158 MET cc_start: 0.8753 (tpp) cc_final: 0.8518 (tpp) REVERT: D 389 ASP cc_start: 0.8189 (m-30) cc_final: 0.7944 (t0) outliers start: 20 outliers final: 13 residues processed: 197 average time/residue: 0.6160 time to fit residues: 133.5302 Evaluate side-chains 184 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 241 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 756 ASN A1250 GLN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.062131 restraints weight = 24252.964| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.25 r_work: 0.2561 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9265 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14838 Z= 0.278 Angle : 0.658 9.821 20116 Z= 0.344 Chirality : 0.052 0.627 2273 Planarity : 0.004 0.061 2561 Dihedral : 6.703 97.140 2015 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.11 % Favored : 93.73 % Rotamer: Outliers : 2.92 % Allowed : 12.54 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.19), residues: 1801 helix: 0.07 (0.48), residues: 126 sheet: 0.36 (0.20), residues: 597 loop : -1.09 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1232 TYR 0.016 0.001 TYR D 43 PHE 0.013 0.002 PHE D 192 TRP 0.010 0.001 TRP D 312 HIS 0.006 0.001 HIS A 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.28 (14830) covalent geometry : angle 0.65807 / 0.34 (20110) hydrogen bonds : bond 0.05498 / 3.75 ( 431) hydrogen bonds : angle 6.29325 / 4.25 ( 1119) metal coordination : bond 0.02275 / 1.23 ( 8) metal coordination : angle 0.95465 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.594 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: A 817 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.7824 (ptm-80) REVERT: A 925 ASN cc_start: 0.8368 (t0) cc_final: 0.8094 (t0) REVERT: D 304 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8926 (mp0) outliers start: 47 outliers final: 20 residues processed: 205 average time/residue: 0.6334 time to fit residues: 142.7628 Evaluate side-chains 189 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 259 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** D 363 HIS ** 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 = 0.3091 r_free = 0.3091 target = 0.084326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.066333 restraints weight = 24177.420| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.25 r_work: 0.2637 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14838 Z= 0.117 Angle : 0.539 8.874 20116 Z= 0.283 Chirality : 0.046 0.192 2273 Planarity : 0.004 0.060 2561 Dihedral : 6.307 127.009 2007 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.05 % Favored : 94.78 % Rotamer: Outliers : 2.79 % Allowed : 12.85 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.19), residues: 1801 helix: -0.07 (0.45), residues: 132 sheet: 0.33 (0.21), residues: 583 loop : -1.08 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1232 TYR 0.012 0.001 TYR D 43 PHE 0.014 0.001 PHE D 332 TRP 0.010 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14830) covalent geometry : angle 0.53926 / 0.28 (20110) hydrogen bonds : bond 0.03882 / 2.63 ( 431) hydrogen bonds : angle 5.90505 / 3.95 ( 1119) metal coordination : bond 0.00715 / 0.39 ( 8) metal coordination : angle 0.65139 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.647 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: A 599 TYR cc_start: 0.8799 (m-80) cc_final: 0.8525 (m-80) REVERT: A 817 ARG cc_start: 0.8292 (ptm-80) cc_final: 0.7785 (ptm-80) REVERT: B 27 LEU cc_start: 0.9341 (mt) cc_final: 0.9123 (mp) REVERT: B 38 ASN cc_start: 0.9024 (t0) cc_final: 0.8766 (t0) REVERT: C 549 TYR cc_start: 0.9237 (m-80) cc_final: 0.8995 (m-80) REVERT: D 304 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8917 (mp0) outliers start: 45 outliers final: 23 residues processed: 215 average time/residue: 0.5900 time to fit residues: 140.3324 Evaluate side-chains 201 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 ARG Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain F residue 216 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** D 363 HIS ** 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 = 0.3035 r_free = 0.3035 target = 0.081020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.062883 restraints weight = 24320.967| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.24 r_work: 0.2572 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14838 Z= 0.219 Angle : 0.598 9.289 20116 Z= 0.313 Chirality : 0.049 0.219 2273 Planarity : 0.004 0.061 2561 Dihedral : 6.506 138.317 2005 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.16 % Favored : 93.67 % Rotamer: Outliers : 3.91 % Allowed : 13.04 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.19), residues: 1801 helix: -0.32 (0.44), residues: 139 sheet: 0.12 (0.20), residues: 611 loop : -1.02 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1232 TYR 0.016 0.001 TYR D 43 PHE 0.012 0.001 PHE A1218 TRP 0.009 0.001 TRP D 246 HIS 0.004 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (14830) covalent geometry : angle 0.59801 / 0.31 (20110) hydrogen bonds : bond 0.04315 / 2.93 ( 431) hydrogen bonds : angle 5.88961 / 3.97 ( 1119) metal coordination : bond 0.01784 / 0.96 ( 8) metal coordination : angle 1.04224 / 0.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 177 time to evaluate : 0.624 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: A 727 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: A 939 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: B 38 ASN cc_start: 0.9009 (t0) cc_final: 0.8682 (t0) REVERT: F 254 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8770 (mmmt) outliers start: 63 outliers final: 30 residues processed: 217 average time/residue: 0.6300 time to fit residues: 150.8041 Evaluate side-chains 196 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 ARG Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 259 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 179 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN D 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.084251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.066303 restraints weight = 24221.292| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.25 r_work: 0.2641 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14838 Z= 0.117 Angle : 0.537 8.729 20116 Z= 0.281 Chirality : 0.046 0.201 2273 Planarity : 0.004 0.061 2561 Dihedral : 6.164 132.406 2003 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 3.41 % Allowed : 14.46 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.92 (0.19), residues: 1801 helix: -0.48 (0.42), residues: 152 sheet: 0.20 (0.21), residues: 580 loop : -1.11 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 612 TYR 0.011 0.001 TYR D 43 PHE 0.013 0.001 PHE D 332 TRP 0.010 0.001 TRP D 312 HIS 0.002 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14830) covalent geometry : angle 0.53655 / 0.28 (20110) hydrogen bonds : bond 0.03494 / 2.37 ( 431) hydrogen bonds : angle 5.69131 / 3.82 ( 1119) metal coordination : bond 0.00643 / 0.34 ( 8) metal coordination : angle 0.65506 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.631 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 93 LEU cc_start: 0.9223 (mm) cc_final: 0.9004 (mm) REVERT: A 116 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: A 571 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.6059 (mm) REVERT: A 727 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: A 817 ARG cc_start: 0.8261 (ptm-80) cc_final: 0.7771 (ptm-80) REVERT: B 38 ASN cc_start: 0.9007 (t0) cc_final: 0.8663 (t0) REVERT: C 549 TYR cc_start: 0.9292 (m-80) cc_final: 0.8998 (m-80) REVERT: F 254 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8743 (mmmt) outliers start: 55 outliers final: 28 residues processed: 214 average time/residue: 0.6118 time to fit residues: 144.8432 Evaluate side-chains 198 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 259 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 0.0570 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A1246 ASN D 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.082365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.064319 restraints weight = 24703.589| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.25 r_work: 0.2604 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9237 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14838 Z= 0.170 Angle : 0.564 9.022 20116 Z= 0.294 Chirality : 0.047 0.233 2273 Planarity : 0.004 0.061 2561 Dihedral : 6.283 136.035 2003 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 3.35 % Allowed : 15.52 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.19), residues: 1801 helix: -0.40 (0.43), residues: 145 sheet: 0.10 (0.20), residues: 597 loop : -1.05 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.014 0.001 TYR D 43 PHE 0.011 0.001 PHE D 192 TRP 0.009 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (14830) covalent geometry : angle 0.56349 / 0.29 (20110) hydrogen bonds : bond 0.03788 / 2.58 ( 431) hydrogen bonds : angle 5.68427 / 3.83 ( 1119) metal coordination : bond 0.01239 / 0.66 ( 8) metal coordination : angle 0.82869 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.480 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8652 (pm20) REVERT: A 571 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.6124 (mm) REVERT: B 27 LEU cc_start: 0.9349 (mt) cc_final: 0.9119 (mp) REVERT: B 38 ASN cc_start: 0.8980 (t0) cc_final: 0.8609 (t0) REVERT: C 549 TYR cc_start: 0.9300 (m-80) cc_final: 0.9056 (m-80) REVERT: F 254 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8777 (mmmt) outliers start: 54 outliers final: 33 residues processed: 210 average time/residue: 0.5737 time to fit residues: 133.3287 Evaluate side-chains 206 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 263 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.083083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.065099 restraints weight = 24488.732| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.25 r_work: 0.2626 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9227 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14838 Z= 0.143 Angle : 0.555 8.810 20116 Z= 0.289 Chirality : 0.047 0.236 2273 Planarity : 0.004 0.061 2561 Dihedral : 6.224 134.927 2003 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.44 % Favored : 94.39 % Rotamer: Outliers : 3.10 % Allowed : 15.89 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.19), residues: 1801 helix: -0.44 (0.42), residues: 151 sheet: 0.06 (0.20), residues: 597 loop : -1.09 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.013 0.001 TYR D 43 PHE 0.011 0.001 PHE D 332 TRP 0.010 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (14830) covalent geometry : angle 0.55487 / 0.29 (20110) hydrogen bonds : bond 0.03612 / 2.45 ( 431) hydrogen bonds : angle 5.65111 / 3.81 ( 1119) metal coordination : bond 0.01018 / 0.54 ( 8) metal coordination : angle 0.80057 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.724 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: A 571 ILE cc_start: 0.6345 (OUTLIER) cc_final: 0.6093 (mm) REVERT: A 817 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.7810 (ptm-80) REVERT: A 938 LEU cc_start: 0.9451 (tt) cc_final: 0.9217 (tp) REVERT: A 939 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8036 (m-30) REVERT: B 27 LEU cc_start: 0.9349 (mt) cc_final: 0.9106 (mp) REVERT: B 38 ASN cc_start: 0.8978 (t0) cc_final: 0.8594 (t0) REVERT: C 549 TYR cc_start: 0.9296 (m-80) cc_final: 0.9027 (m-80) REVERT: F 254 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8739 (mmmt) outliers start: 50 outliers final: 31 residues processed: 213 average time/residue: 0.5745 time to fit residues: 135.7557 Evaluate side-chains 204 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 263 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 86 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 535 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.082629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.064616 restraints weight = 24551.550| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.25 r_work: 0.2617 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9235 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14838 Z= 0.163 Angle : 0.569 8.887 20116 Z= 0.295 Chirality : 0.047 0.261 2273 Planarity : 0.004 0.061 2561 Dihedral : 6.286 136.233 2003 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 3.29 % Allowed : 16.20 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.19), residues: 1801 helix: -0.48 (0.42), residues: 151 sheet: 0.08 (0.20), residues: 599 loop : -1.07 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.014 0.001 TYR D 43 PHE 0.011 0.001 PHE D 192 TRP 0.009 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (14830) covalent geometry : angle 0.56911 / 0.30 (20110) hydrogen bonds : bond 0.03706 / 2.52 ( 431) hydrogen bonds : angle 5.65534 / 3.81 ( 1119) metal coordination : bond 0.01184 / 0.62 ( 8) metal coordination : angle 0.90894 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 0.620 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: A 571 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.6110 (mm) REVERT: A 938 LEU cc_start: 0.9455 (tt) cc_final: 0.9211 (tp) REVERT: A 939 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: B 27 LEU cc_start: 0.9351 (mt) cc_final: 0.9114 (mp) REVERT: B 38 ASN cc_start: 0.8981 (t0) cc_final: 0.8592 (t0) REVERT: C 548 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8678 (t0) REVERT: D 304 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8964 (mp0) REVERT: F 254 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8779 (mmmt) outliers start: 53 outliers final: 32 residues processed: 207 average time/residue: 0.6186 time to fit residues: 141.6757 Evaluate side-chains 208 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 263 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 754 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.065177 restraints weight = 24793.090| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 2.26 r_work: 0.2631 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9229 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14838 Z= 0.148 Angle : 0.568 8.764 20116 Z= 0.295 Chirality : 0.047 0.280 2273 Planarity : 0.004 0.061 2561 Dihedral : 6.248 134.874 2003 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.34 % Rotamer: Outliers : 2.86 % Allowed : 16.57 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.97 (0.19), residues: 1801 helix: -0.45 (0.42), residues: 151 sheet: 0.07 (0.20), residues: 596 loop : -1.11 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1267 TYR 0.013 0.001 TYR D 43 PHE 0.011 0.001 PHE A 194 TRP 0.009 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14830) covalent geometry : angle 0.56790 / 0.30 (20110) hydrogen bonds : bond 0.03594 / 2.44 ( 431) hydrogen bonds : angle 5.62248 / 3.79 ( 1119) metal coordination : bond 0.01022 / 0.54 ( 8) metal coordination : angle 0.83550 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.479 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: A 571 ILE cc_start: 0.6337 (OUTLIER) cc_final: 0.6111 (mm) REVERT: A 817 ARG cc_start: 0.8303 (ptm-80) cc_final: 0.7761 (ptm-80) REVERT: A 938 LEU cc_start: 0.9460 (tt) cc_final: 0.9213 (tp) REVERT: A 939 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: B 27 LEU cc_start: 0.9348 (mt) cc_final: 0.9137 (mp) REVERT: B 38 ASN cc_start: 0.8984 (t0) cc_final: 0.8592 (t0) REVERT: C 548 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8686 (t0) REVERT: D 304 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8953 (mp0) REVERT: F 254 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8744 (mmmt) outliers start: 46 outliers final: 31 residues processed: 205 average time/residue: 0.6009 time to fit residues: 136.0267 Evaluate side-chains 204 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 263 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 84 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.0270 chunk 102 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 754 GLN ** D 218 HIS ** 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 = 0.3097 r_free = 0.3097 target = 0.084339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.066330 restraints weight = 24521.284| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.25 r_work: 0.2655 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9212 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14838 Z= 0.124 Angle : 0.555 8.863 20116 Z= 0.288 Chirality : 0.046 0.263 2273 Planarity : 0.004 0.062 2561 Dihedral : 6.107 132.636 2003 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.34 % Rotamer: Outliers : 2.61 % Allowed : 17.07 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.19), residues: 1801 helix: -0.59 (0.41), residues: 157 sheet: 0.15 (0.20), residues: 593 loop : -1.12 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 612 TYR 0.012 0.001 TYR D 43 PHE 0.013 0.001 PHE A 194 TRP 0.010 0.001 TRP D 312 HIS 0.005 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (14830) covalent geometry : angle 0.55534 / 0.29 (20110) hydrogen bonds : bond 0.03399 / 2.30 ( 431) hydrogen bonds : angle 5.53083 / 3.72 ( 1119) metal coordination : bond 0.00748 / 0.39 ( 8) metal coordination : angle 0.77950 / 0.38 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3602 Ramachandran restraints generated. 1801 Oldfield, 0 Emsley, 1801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.588 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: A 571 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6081 (mm) REVERT: A 938 LEU cc_start: 0.9458 (tt) cc_final: 0.9213 (tp) REVERT: A 939 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: B 27 LEU cc_start: 0.9332 (mt) cc_final: 0.9093 (mp) REVERT: B 38 ASN cc_start: 0.8978 (t0) cc_final: 0.8584 (t0) REVERT: C 548 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8728 (t0) REVERT: F 254 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8703 (mmmt) outliers start: 42 outliers final: 30 residues processed: 209 average time/residue: 0.6188 time to fit residues: 142.8526 Evaluate side-chains 207 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 ARG Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain F residue 254 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 164 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN A 256 ASN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 ASN ** 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 = 0.3023 r_free = 0.3023 target = 0.080063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.061943 restraints weight = 24753.400| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.24 r_work: 0.2556 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9272 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 14838 Z= 0.292 Angle : 0.664 9.817 20116 Z= 0.345 Chirality : 0.051 0.332 2273 Planarity : 0.004 0.063 2561 Dihedral : 6.673 141.032 2003 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.39 % Favored : 93.45 % Rotamer: Outliers : 2.86 % Allowed : 17.01 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.19), residues: 1801 helix: -0.22 (0.45), residues: 132 sheet: 0.01 (0.20), residues: 603 loop : -1.05 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 612 TYR 0.016 0.002 TYR A1266 PHE 0.015 0.002 PHE A 194 TRP 0.010 0.001 TRP D 246 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.29 (14830) covalent geometry : angle 0.66353 / 0.35 (20110) hydrogen bonds : bond 0.04370 / 2.98 ( 431) hydrogen bonds : angle 5.79343 / 3.93 ( 1119) metal coordination : bond 0.02172 / 1.16 ( 8) metal coordination : angle 1.26641 / 0.67 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.51 seconds wall clock time: 87 minutes 22.58 seconds (5242.58 seconds total)