Starting phenix.real_space_refine (version: dev) on Tue Feb 21 10:42:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgr_14712/02_2023/7zgr_14712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgr_14712/02_2023/7zgr_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgr_14712/02_2023/7zgr_14712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgr_14712/02_2023/7zgr_14712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgr_14712/02_2023/7zgr_14712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgr_14712/02_2023/7zgr_14712.pdb" } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A GLU 106": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 1082": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 252": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/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: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'GLU:plan': 1, 'ARG: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: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1} 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, 'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 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: {'GLN:plan1': 1, 'ARG:plan': 2} 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: 8.57, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 6.00 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.15 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: 6.42 Time building geometry restraints manager: 6.50 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: 99.97 - 106.78: 471 106.78 - 113.59: 8181 113.59 - 120.39: 5187 120.39 - 127.20: 6107 127.20 - 134.01: 167 Bond angle restraints: 20113 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 20108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 8004 17.61 - 35.22: 723 35.22 - 52.83: 173 52.83 - 70.44: 32 70.44 - 88.06: 13 Dihedral angle restraints: 8945 sinusoidal: 3611 harmonic: 5334 Sorted by residual: dihedral pdb=" CA GLU A1155 " pdb=" C GLU A1155 " pdb=" N PRO A1156 " pdb=" CA PRO A1156 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA VAL A 663 " pdb=" C VAL A 663 " pdb=" N MET A 664 " pdb=" CA MET A 664 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP B 30 " pdb=" CB ASP B 30 " pdb=" CG ASP B 30 " pdb=" OD1 ASP B 30 " ideal model delta sinusoidal sigma weight residual -30.00 -89.05 59.05 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 8942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1725 0.049 - 0.097: 389 0.097 - 0.146: 152 0.146 - 0.195: 4 0.195 - 0.244: 3 Chirality restraints: 2273 Sorted by residual: 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 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA VAL D 264 " pdb=" N VAL D 264 " pdb=" C VAL D 264 " pdb=" CB VAL D 264 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.92e-01 ... (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 2.520 nonbonded pdb=" N GLU A 697 " pdb=" OE1 GLU A 697 " model vdw 2.205 2.520 nonbonded pdb=" OH TYR A1266 " pdb=" O PRO A1306 " model vdw 2.206 2.440 nonbonded pdb=" O ASP A 583 " pdb=" OG SER A 601 " model vdw 2.216 2.440 nonbonded pdb=" NZ LYS A 84 " pdb=" OE2 GLU A1291 " model vdw 2.252 2.520 ... (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 ========== 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 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. 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.450 Check model and map are aligned: 0.190 Process input model: 44.160 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.760 ------------------------------------------------------------------------------- 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 14830 Z= 0.219 Angle : 0.565 9.712 20113 Z= 0.321 Chirality : 0.046 0.244 2273 Planarity : 0.004 0.063 2561 Dihedral : 14.682 88.056 5489 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (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 *********************** 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 fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 1.669 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 20 outliers final: 13 residues processed: 197 average time/residue: 1.3130 time to fit residues: 284.4960 Evaluate side-chains 184 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.944 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.2109 time to fit residues: 2.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.0050 chunk 92 optimal weight: 0.0870 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN A1250 GLN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 14830 Z= 0.148 Angle : 0.511 8.936 20113 Z= 0.270 Chirality : 0.045 0.198 2273 Planarity : 0.004 0.058 2561 Dihedral : 4.689 39.814 1994 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1801 helix: -0.17 (0.45), residues: 138 sheet: 0.57 (0.21), residues: 594 loop : -1.05 (0.18), residues: 1069 *********************** 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 236 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 1.889 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 40 outliers final: 17 residues processed: 220 average time/residue: 1.2213 time to fit residues: 297.7377 Evaluate side-chains 189 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.9523 time to fit residues: 7.8755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A1246 ASN ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.092 14830 Z= 0.673 Angle : 0.722 10.243 20113 Z= 0.379 Chirality : 0.054 0.238 2273 Planarity : 0.005 0.060 2561 Dihedral : 5.691 33.844 1994 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.66 % Favored : 93.17 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1801 helix: -0.03 (0.47), residues: 125 sheet: 0.22 (0.20), residues: 601 loop : -1.12 (0.18), residues: 1075 *********************** 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 234 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 170 time to evaluate : 1.882 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 64 outliers final: 30 residues processed: 213 average time/residue: 1.2868 time to fit residues: 302.8977 Evaluate side-chains 189 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 0.4098 time to fit residues: 5.8953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 109 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9226 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14830 Z= 0.197 Angle : 0.540 9.172 20113 Z= 0.284 Chirality : 0.046 0.181 2273 Planarity : 0.004 0.058 2561 Dihedral : 5.170 36.920 1994 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.34 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1801 helix: 0.04 (0.47), residues: 126 sheet: 0.27 (0.20), residues: 596 loop : -1.10 (0.18), residues: 1079 *********************** 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 fitting. rotamer outliers: 64 poor density : 176 time to evaluate : 1.669 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 64 outliers final: 33 residues processed: 221 average time/residue: 1.2361 time to fit residues: 301.9335 Evaluate side-chains 201 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 8 average time/residue: 0.5344 time to fit residues: 7.7434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 129 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 120 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 14830 Z= 0.169 Angle : 0.520 9.188 20113 Z= 0.270 Chirality : 0.045 0.204 2273 Planarity : 0.004 0.058 2561 Dihedral : 4.889 38.273 1994 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.94 % Favored : 93.89 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1801 helix: 0.02 (0.45), residues: 133 sheet: 0.26 (0.21), residues: 591 loop : -1.12 (0.18), residues: 1077 *********************** 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 236 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.978 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 49 outliers final: 32 residues processed: 224 average time/residue: 1.3170 time to fit residues: 325.6735 Evaluate side-chains 203 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 1.0087 time to fit residues: 7.0090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.0470 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 729 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 GLN B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 14830 Z= 0.175 Angle : 0.520 9.158 20113 Z= 0.270 Chirality : 0.045 0.217 2273 Planarity : 0.004 0.058 2561 Dihedral : 4.822 38.664 1994 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.34 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1801 helix: 0.08 (0.45), residues: 132 sheet: 0.30 (0.21), residues: 579 loop : -1.07 (0.18), residues: 1090 *********************** 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 232 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 1.773 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 51 outliers final: 33 residues processed: 217 average time/residue: 1.2570 time to fit residues: 302.2438 Evaluate side-chains 205 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 0.5713 time to fit residues: 4.3312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 0.0370 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14830 Z= 0.218 Angle : 0.537 9.291 20113 Z= 0.277 Chirality : 0.046 0.240 2273 Planarity : 0.004 0.058 2561 Dihedral : 4.901 38.490 1994 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.27 % Favored : 93.56 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1801 helix: 0.09 (0.45), residues: 132 sheet: 0.22 (0.21), residues: 593 loop : -1.03 (0.18), residues: 1076 *********************** 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 228 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.756 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 54 outliers final: 37 residues processed: 212 average time/residue: 1.3045 time to fit residues: 305.5214 Evaluate side-chains 211 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 29 residues processed: 8 average time/residue: 0.6056 time to fit residues: 8.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 729 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9220 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14830 Z= 0.228 Angle : 0.545 9.265 20113 Z= 0.282 Chirality : 0.046 0.262 2273 Planarity : 0.004 0.059 2561 Dihedral : 4.933 38.212 1994 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.16 % Favored : 93.67 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1801 helix: 0.12 (0.45), residues: 132 sheet: 0.22 (0.21), residues: 593 loop : -1.04 (0.18), residues: 1076 *********************** 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 228 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 177 time to evaluate : 1.901 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 51 outliers final: 34 residues processed: 213 average time/residue: 1.2784 time to fit residues: 300.9895 Evaluate side-chains 205 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 29 residues processed: 5 average time/residue: 0.9587 time to fit residues: 8.0331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.5980 chunk 166 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14830 Z= 0.182 Angle : 0.533 9.362 20113 Z= 0.275 Chirality : 0.046 0.272 2273 Planarity : 0.004 0.058 2561 Dihedral : 4.816 38.691 1994 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.22 % Favored : 93.61 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 1801 helix: 0.01 (0.44), residues: 138 sheet: 0.29 (0.21), residues: 592 loop : -1.07 (0.18), residues: 1071 *********************** 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 221 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.813 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 42 outliers final: 32 residues processed: 212 average time/residue: 1.3001 time to fit residues: 305.0963 Evaluate side-chains 205 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 3 average time/residue: 0.5823 time to fit residues: 4.8300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14830 Z= 0.183 Angle : 0.535 9.913 20113 Z= 0.275 Chirality : 0.046 0.268 2273 Planarity : 0.004 0.058 2561 Dihedral : 4.783 38.810 1994 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.22 % Favored : 93.61 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1801 helix: -0.01 (0.44), residues: 138 sheet: 0.24 (0.20), residues: 596 loop : -1.05 (0.18), residues: 1067 ********************** 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 210 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.789 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 35 outliers final: 30 residues processed: 205 average time/residue: 1.3369 time to fit residues: 302.4730 Evaluate side-chains 202 residues out of total 1654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.1838 time to fit residues: 2.8038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 0.4980 chunk 59 optimal weight: 0.0470 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.0060 chunk 125 optimal weight: 6.9990 overall best weight: 0.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.067603 restraints weight = 24511.653| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.24 r_work: 0.2674 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 14830 Z= 0.152 Angle : 0.524 9.905 20113 Z= 0.270 Chirality : 0.045 0.295 2273 Planarity : 0.003 0.058 2561 Dihedral : 4.681 38.935 1994 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.94 % Favored : 93.89 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1801 helix: 0.03 (0.45), residues: 138 sheet: 0.26 (0.21), residues: 591 loop : -1.03 (0.18), residues: 1072 =============================================================================== Job complete usr+sys time: 5430.30 seconds wall clock time: 97 minutes 6.84 seconds (5826.84 seconds total)