Starting phenix.real_space_refine on Wed Mar 4 16:20:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zgr_14712/03_2026/7zgr_14712.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgr_14712/03_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_14712/03_2026/7zgr_14712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgr_14712/03_2026/7zgr_14712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zgr_14712/03_2026/7zgr_14712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgr_14712/03_2026/7zgr_14712.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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, '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: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: 2.91, per 1000 atoms: 0.20 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: 1.24 Conformation dependent library (CDL) restraints added in 586.4 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: 0.77 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: 3.20 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: 19769 1.94 - 3.88: 313 3.88 - 5.83: 27 5.83 - 7.77: 3 7.77 - 9.71: 1 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: 8005 17.61 - 35.22: 723 35.22 - 52.83: 173 52.83 - 70.44: 33 70.44 - 88.06: 13 Dihedral angle restraints: 8947 sinusoidal: 3613 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 8944 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 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: 3.230 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.620 Find NCS groups from input model: 0.060 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:8.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 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 : 0.565 9.712 20119 Z= 0.321 Chirality : 0.046 0.244 2273 Planarity : 0.004 0.063 2561 Dihedral : 14.700 88.056 5491 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 covalent geometry : bond 0.00335 (14830) covalent geometry : angle 0.56482 (20113) hydrogen bonds : bond 0.22644 ( 431) hydrogen bonds : angle 8.67897 ( 1119) metal coordination : bond 0.00628 ( 8) metal coordination : angle 0.87965 ( 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 : 0.624 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: 0.6232 time to fit residues: 134.7432 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 : 0.539 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3024 r_free = 0.3024 target = 0.080274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.062098 restraints weight = 24397.591| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.26 r_work: 0.2550 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.0941 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= 0.275 Angle : 0.628 9.207 20119 Z= 0.334 Chirality : 0.049 0.220 2273 Planarity : 0.004 0.060 2561 Dihedral : 6.236 58.356 2018 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.16 % Favored : 93.67 % Rotamer: Outliers : 2.79 % Allowed : 12.54 % Favored : 84.67 % 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: -0.73 (0.19), residues: 1801 helix: 0.08 (0.48), residues: 126 sheet: 0.38 (0.20), residues: 602 loop : -1.09 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 0.005 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00637 (14830) covalent geometry : angle 0.62792 (20113) hydrogen bonds : bond 0.05632 ( 431) hydrogen bonds : angle 6.36251 ( 1119) metal coordination : bond 0.02211 ( 8) metal coordination : angle 0.84694 ( 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 225 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.558 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8129 (pm20) REVERT: A 817 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7787 (ptm-80) REVERT: D 304 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8912 (mp0) outliers start: 45 outliers final: 18 residues processed: 203 average time/residue: 0.6132 time to fit residues: 136.2723 Evaluate side-chains 189 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3074 r_free = 0.3074 target = 0.083244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.065318 restraints weight = 24248.894| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.25 r_work: 0.2632 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14838 Z= 0.124 Angle : 0.544 8.805 20119 Z= 0.287 Chirality : 0.046 0.188 2273 Planarity : 0.004 0.060 2561 Dihedral : 5.676 59.022 2008 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.66 % Favored : 94.17 % 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: -0.77 (0.19), residues: 1801 helix: -0.06 (0.45), residues: 132 sheet: 0.30 (0.20), residues: 600 loop : -1.07 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1232 TYR 0.012 0.001 TYR D 43 PHE 0.013 0.001 PHE D 332 TRP 0.009 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00273 (14830) covalent geometry : angle 0.54364 (20113) hydrogen bonds : bond 0.04066 ( 431) hydrogen bonds : angle 5.99212 ( 1119) metal coordination : bond 0.00857 ( 8) metal coordination : angle 0.70598 ( 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 234 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.500 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: A 817 ARG cc_start: 0.8301 (ptm-80) cc_final: 0.7787 (ptm-80) REVERT: B 27 LEU cc_start: 0.9348 (mt) cc_final: 0.9143 (mp) REVERT: B 38 ASN cc_start: 0.9017 (t0) cc_final: 0.8727 (t0) REVERT: D 304 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8907 (mp0) outliers start: 45 outliers final: 24 residues processed: 212 average time/residue: 0.6123 time to fit residues: 142.6032 Evaluate side-chains 200 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain F residue 259 ASP 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: 3.9990 chunk 148 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 146 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3055 r_free = 0.3055 target = 0.082152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.064244 restraints weight = 24385.688| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.25 r_work: 0.2607 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1153 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= 0.168 Angle : 0.559 9.126 20119 Z= 0.294 Chirality : 0.047 0.205 2273 Planarity : 0.004 0.060 2561 Dihedral : 5.694 58.262 2008 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.89 % Favored : 93.95 % Rotamer: Outliers : 3.48 % Allowed : 13.10 % Favored : 83.43 % 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: -0.84 (0.19), residues: 1801 helix: -0.32 (0.44), residues: 139 sheet: 0.14 (0.20), residues: 611 loop : -1.01 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1232 TYR 0.014 0.001 TYR D 43 PHE 0.012 0.001 PHE D 192 TRP 0.009 0.001 TRP D 312 HIS 0.004 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00385 (14830) covalent geometry : angle 0.55919 (20113) hydrogen bonds : bond 0.04005 ( 431) hydrogen bonds : angle 5.83221 ( 1119) metal coordination : bond 0.01420 ( 8) metal coordination : angle 0.84897 ( 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 239 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.461 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: 0.8101 (pm20) REVERT: B 27 LEU cc_start: 0.9363 (mt) cc_final: 0.9143 (mp) REVERT: B 38 ASN cc_start: 0.9009 (t0) cc_final: 0.8675 (t0) outliers start: 56 outliers final: 30 residues processed: 216 average time/residue: 0.5924 time to fit residues: 140.9416 Evaluate side-chains 198 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 384 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 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 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 259 ASP Chi-restraints excluded: chain F residue 263 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 145 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A1145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.084724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.066950 restraints weight = 24238.629| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.24 r_work: 0.2660 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14838 Z= 0.113 Angle : 0.532 8.855 20119 Z= 0.278 Chirality : 0.046 0.206 2273 Planarity : 0.004 0.059 2561 Dihedral : 5.451 58.144 2006 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 3.10 % Allowed : 14.65 % Favored : 82.25 % 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: -0.90 (0.19), residues: 1801 helix: -0.60 (0.41), residues: 157 sheet: 0.22 (0.21), residues: 581 loop : -1.07 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.003 0.000 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00253 (14830) covalent geometry : angle 0.53178 (20113) hydrogen bonds : bond 0.03431 ( 431) hydrogen bonds : angle 5.64861 ( 1119) metal coordination : bond 0.00704 ( 8) metal coordination : angle 0.67527 ( 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: 50 poor density : 183 time to evaluate : 0.546 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: A 817 ARG cc_start: 0.8259 (ptm-80) cc_final: 0.7766 (ptm-80) REVERT: A 979 TYR cc_start: 0.8898 (p90) cc_final: 0.8660 (p90) REVERT: B 27 LEU cc_start: 0.9318 (mt) cc_final: 0.9110 (mp) REVERT: B 38 ASN cc_start: 0.8992 (t0) cc_final: 0.8637 (t0) outliers start: 50 outliers final: 24 residues processed: 213 average time/residue: 0.5718 time to fit residues: 133.8149 Evaluate side-chains 196 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 198 SER Chi-restraints excluded: chain A residue 199 VAL 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 661 VAL 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 1089 THR 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 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain F residue 216 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: 0.5980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN 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 = 0.082866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.064823 restraints weight = 24395.621| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.26 r_work: 0.2620 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.1275 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= 0.157 Angle : 0.555 9.234 20119 Z= 0.289 Chirality : 0.046 0.236 2273 Planarity : 0.004 0.060 2561 Dihedral : 5.541 58.216 2006 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.34 % Rotamer: Outliers : 3.66 % Allowed : 15.21 % 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: -0.93 (0.19), residues: 1801 helix: -0.44 (0.42), residues: 151 sheet: 0.10 (0.20), residues: 597 loop : -1.08 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 612 TYR 0.014 0.001 TYR D 43 PHE 0.011 0.001 PHE B 61 TRP 0.009 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00362 (14830) covalent geometry : angle 0.55499 (20113) hydrogen bonds : bond 0.03702 ( 431) hydrogen bonds : angle 5.64437 ( 1119) metal coordination : bond 0.01239 ( 8) metal coordination : angle 0.86318 ( 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 238 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 179 time to evaluate : 0.582 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8649 (pm20) REVERT: A 299 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9045 (mp) REVERT: A 571 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.6073 (mm) REVERT: A 939 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 27 LEU cc_start: 0.9357 (mt) cc_final: 0.9151 (mp) REVERT: B 38 ASN cc_start: 0.8962 (t0) cc_final: 0.8576 (t0) REVERT: C 548 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8619 (t0) outliers start: 59 outliers final: 32 residues processed: 219 average time/residue: 0.5860 time to fit residues: 141.2243 Evaluate side-chains 210 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 299 LEU 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 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 C residue 548 ASP Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 200 ILE 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 259 ASP 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: 2.9990 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 112 optimal weight: 0.0980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.065618 restraints weight = 24506.998| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.25 r_work: 0.2641 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14838 Z= 0.135 Angle : 0.554 8.900 20119 Z= 0.286 Chirality : 0.046 0.245 2273 Planarity : 0.004 0.060 2561 Dihedral : 5.501 58.189 2006 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.16 % Favored : 94.67 % Rotamer: Outliers : 3.17 % Allowed : 16.14 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.88 (0.19), residues: 1801 helix: -0.46 (0.42), residues: 150 sheet: 0.13 (0.20), residues: 587 loop : -1.03 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.012 0.001 TYR D 43 PHE 0.011 0.001 PHE D 332 TRP 0.009 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00310 (14830) covalent geometry : angle 0.55357 (20113) hydrogen bonds : bond 0.03540 ( 431) hydrogen bonds : angle 5.61095 ( 1119) metal coordination : bond 0.01025 ( 8) metal coordination : angle 0.84059 ( 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 227 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 0.365 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8656 (pm20) REVERT: A 299 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9012 (mp) REVERT: A 571 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.6073 (mm) REVERT: A 817 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7810 (ptm-80) REVERT: A 938 LEU cc_start: 0.9452 (tt) cc_final: 0.9217 (tp) REVERT: A 939 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: B 27 LEU cc_start: 0.9358 (mt) cc_final: 0.9150 (mp) REVERT: B 38 ASN cc_start: 0.8969 (t0) cc_final: 0.8579 (t0) REVERT: F 254 LYS cc_start: 0.8928 (mptm) cc_final: 0.8696 (mmmt) outliers start: 51 outliers final: 34 residues processed: 212 average time/residue: 0.5856 time to fit residues: 136.8787 Evaluate side-chains 208 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 299 LEU 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 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 B residue 90 ARG Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 131 MET 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 259 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 136 optimal weight: 0.0170 chunk 149 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9224 ------------------------------------------------------------------------------- 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 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.064987 restraints weight = 24636.027| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.25 r_work: 0.2626 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14838 Z= 0.150 Angle : 0.562 9.316 20119 Z= 0.291 Chirality : 0.046 0.268 2273 Planarity : 0.004 0.061 2561 Dihedral : 5.540 58.218 2006 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 3.23 % Allowed : 16.26 % 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: -0.90 (0.19), residues: 1801 helix: -0.49 (0.42), residues: 150 sheet: 0.06 (0.20), residues: 601 loop : -1.01 (0.19), residues: 1050 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 A 194 TRP 0.010 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00344 (14830) covalent geometry : angle 0.56185 (20113) hydrogen bonds : bond 0.03612 ( 431) hydrogen bonds : angle 5.60871 ( 1119) metal coordination : bond 0.01212 ( 8) metal coordination : angle 0.91596 ( 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 226 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.502 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (pm20) REVERT: A 571 ILE cc_start: 0.6319 (OUTLIER) cc_final: 0.6086 (mm) REVERT: A 817 ARG cc_start: 0.8255 (ptm-80) cc_final: 0.7778 (ptm-80) REVERT: A 938 LEU cc_start: 0.9459 (tt) cc_final: 0.9209 (tp) REVERT: A 939 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: A 1305 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7473 (mtp85) REVERT: B 38 ASN cc_start: 0.8974 (t0) cc_final: 0.8583 (t0) REVERT: D 304 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8958 (mp0) REVERT: F 254 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8690 (mmmt) outliers start: 52 outliers final: 33 residues processed: 211 average time/residue: 0.5938 time to fit residues: 138.0557 Evaluate side-chains 206 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 D residue 29 GLN Chi-restraints excluded: chain D residue 131 MET 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 D residue 352 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 62 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN D 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.065631 restraints weight = 24832.545| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.26 r_work: 0.2643 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14838 Z= 0.134 Angle : 0.563 9.436 20119 Z= 0.291 Chirality : 0.046 0.285 2273 Planarity : 0.004 0.061 2561 Dihedral : 5.492 58.187 2006 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.39 % Favored : 94.45 % Rotamer: Outliers : 2.92 % Allowed : 17.26 % Favored : 79.83 % 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: -0.88 (0.19), residues: 1801 helix: -0.45 (0.42), residues: 150 sheet: 0.14 (0.20), residues: 585 loop : -1.03 (0.18), residues: 1066 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 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00308 (14830) covalent geometry : angle 0.56313 (20113) hydrogen bonds : bond 0.03482 ( 431) hydrogen bonds : angle 5.57071 ( 1119) metal coordination : bond 0.01062 ( 8) metal coordination : angle 0.76431 ( 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 221 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.570 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: A 571 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.6083 (mm) REVERT: A 817 ARG cc_start: 0.8259 (ptm-80) cc_final: 0.7787 (ptm-80) REVERT: A 938 LEU cc_start: 0.9464 (tt) cc_final: 0.9227 (tp) REVERT: A 939 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: B 38 ASN cc_start: 0.8967 (t0) cc_final: 0.8569 (t0) REVERT: B 76 LYS cc_start: 0.9236 (mttm) cc_final: 0.9031 (mttt) REVERT: C 548 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8640 (t0) REVERT: D 304 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8977 (mp0) REVERT: F 254 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8672 (mmmt) outliers start: 47 outliers final: 32 residues processed: 204 average time/residue: 0.5719 time to fit residues: 128.1801 Evaluate side-chains 204 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 131 MET 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 D residue 352 CYS 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 84 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 754 GLN D 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.083605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.065767 restraints weight = 24700.799| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.25 r_work: 0.2649 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14838 Z= 0.136 Angle : 0.563 9.849 20119 Z= 0.291 Chirality : 0.046 0.273 2273 Planarity : 0.004 0.061 2561 Dihedral : 5.478 58.173 2006 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 2.92 % Allowed : 16.95 % 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: -0.92 (0.19), residues: 1801 helix: -0.59 (0.41), residues: 157 sheet: 0.18 (0.20), residues: 593 loop : -1.09 (0.19), 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 0.003 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00312 (14830) covalent geometry : angle 0.56287 (20113) hydrogen bonds : bond 0.03484 ( 431) hydrogen bonds : angle 5.55357 ( 1119) metal coordination : bond 0.01012 ( 8) metal coordination : angle 0.85943 ( 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 226 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.623 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 116 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: A 571 ILE cc_start: 0.6312 (OUTLIER) cc_final: 0.6098 (mm) REVERT: A 817 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7722 (ptm-80) REVERT: A 938 LEU cc_start: 0.9456 (tt) cc_final: 0.9248 (tp) REVERT: A 939 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: A 979 TYR cc_start: 0.8931 (p90) cc_final: 0.8694 (p90) REVERT: B 27 LEU cc_start: 0.9361 (mt) cc_final: 0.9132 (mp) REVERT: B 38 ASN cc_start: 0.8976 (t0) cc_final: 0.8584 (t0) REVERT: C 548 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8612 (t0) REVERT: F 254 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8665 (mmmt) outliers start: 47 outliers final: 32 residues processed: 213 average time/residue: 0.5940 time to fit residues: 139.3935 Evaluate side-chains 213 residues out of total 1654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 131 MET 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 D residue 352 CYS 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: 2.9990 chunk 143 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 535 ASN A 754 GLN D 211 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.080526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.062512 restraints weight = 24804.167| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.24 r_work: 0.2573 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14838 Z= 0.239 Angle : 0.634 10.446 20119 Z= 0.330 Chirality : 0.049 0.339 2273 Planarity : 0.004 0.062 2561 Dihedral : 5.887 58.371 2006 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.22 % Favored : 93.61 % Rotamer: Outliers : 2.92 % Allowed : 17.07 % Favored : 80.01 % 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: -0.90 (0.19), residues: 1801 helix: -0.21 (0.45), residues: 132 sheet: 0.06 (0.20), residues: 599 loop : -1.04 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 612 TYR 0.015 0.001 TYR A1266 PHE 0.014 0.002 PHE A 194 TRP 0.009 0.001 TRP D 246 HIS 0.004 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00552 (14830) covalent geometry : angle 0.63393 (20113) hydrogen bonds : bond 0.04164 ( 431) hydrogen bonds : angle 5.78585 ( 1119) metal coordination : bond 0.01914 ( 8) metal coordination : angle 1.20386 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4739.24 seconds wall clock time: 81 minutes 44.54 seconds (4904.54 seconds total)