Starting phenix.real_space_refine on Sun Dec 10 07:09:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgq_14711/12_2023/7zgq_14711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgq_14711/12_2023/7zgq_14711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgq_14711/12_2023/7zgq_14711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgq_14711/12_2023/7zgq_14711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgq_14711/12_2023/7zgq_14711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zgq_14711/12_2023/7zgq_14711.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 8771 2.51 5 N 2310 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 178": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13704 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 285 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 33} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 9691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1237, 9691 Classifications: {'peptide': 1237} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 51, 'TRANS': 1185} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 78} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3023 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 19, 'TRANS': 364} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Time building chain proxies: 7.58, per 1000 atoms: 0.55 Number of scatterers: 13704 At special positions: 0 Unit cell: (110.55, 108.9, 114.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2555 8.00 N 2310 7.00 C 8771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.5 seconds 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 28 sheets defined 8.8% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.687A pdb=" N LYS A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.853A pdb=" N GLU A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 Processing helix chain 'A' and resid 1203 through 1207 removed outlier: 4.110A pdb=" N LEU A1207 " --> pdb=" O PRO A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1280 Processing helix chain 'A' and resid 1287 through 1293 Processing helix chain 'A' and resid 1297 through 1301 removed outlier: 4.135A pdb=" N GLY A1301 " --> pdb=" O TYR A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1315 removed outlier: 3.547A pdb=" N ARG A1315 " --> pdb=" O ASN A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1329 removed outlier: 3.505A pdb=" N GLN A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1348 removed outlier: 3.632A pdb=" N GLU A1338 " --> pdb=" O HIS A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1355 removed outlier: 4.084A pdb=" N SER A1352 " --> pdb=" O SER A1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.890A pdb=" N ASN B 63 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.655A pdb=" N LYS B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 92' Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.613A 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: 3.975A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 77 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.619A pdb=" N ILE A 87 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LEU A 102 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 85 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 80 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE A 90 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER A 74 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'A' and resid 1224 through 1231 removed outlier: 3.827A pdb=" N CYS A1226 " --> pdb=" O GLY A1249 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE A1244 " --> pdb=" O PRO A1260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.140A pdb=" N ARG A 41 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU A 50 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 125 Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 218 removed outlier: 6.695A pdb=" N LEU A 230 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 216 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 228 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A 218 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR A 226 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N THR A 248 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS A 275 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR A 250 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE A 273 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 252 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 286 removed outlier: 4.180A pdb=" N GLU A 298 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 310 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP A 303 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN A 309 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASN A 329 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 311 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.945A pdb=" N LEU A 363 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 376 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 388 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU A 378 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LYS A 386 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 405 through 410 removed outlier: 3.721A pdb=" N CYS A 407 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 431 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 504 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 433 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 500 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 513 through 517 removed outlier: 4.193A pdb=" N SER A 513 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 525 through 526 Processing sheet with id=AB3, first strand: chain 'A' and resid 561 through 564 removed outlier: 5.658A pdb=" N ILE A 562 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 915 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 564 " --> pdb=" O VAL A 913 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 574 through 577 removed outlier: 4.983A pdb=" N TYR A 585 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 621 through 625 removed outlier: 3.618A pdb=" N THR A 650 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 658 through 663 Processing sheet with id=AB7, first strand: chain 'A' and resid 704 through 712 removed outlier: 3.599A pdb=" N SER A 706 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 744 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE A 741 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 766 " --> pdb=" O ASN A 756 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU A 797 " --> pdb=" O LYS A 813 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU A 796 " --> pdb=" O LYS A 789 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 789 " --> pdb=" O GLU A 796 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 798 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 787 " --> pdb=" O TYR A 798 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 800 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 785 " --> pdb=" O THR A 800 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 802 " --> pdb=" O LYS A 783 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 851 through 854 Processing sheet with id=AB9, first strand: chain 'A' and resid 944 through 950 removed outlier: 6.592A pdb=" N LEU A 944 " --> pdb=" O CYS A 961 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N CYS A 961 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LYS A 946 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER A 959 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 960 " --> pdb=" O GLY A 992 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N SER A 991 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP A1008 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 993 " --> pdb=" O LYS A1006 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS A1006 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 995 " --> pdb=" O ILE A1004 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1013 through 1023 removed outlier: 6.704A pdb=" N GLY A1039 " --> pdb=" O ASN A1016 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET A1018 " --> pdb=" O ILE A1037 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A1037 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER A1020 " --> pdb=" O TYR A1035 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR A1035 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N MET A1022 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A1033 " --> pdb=" O MET A1022 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU A1034 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL A1059 " --> pdb=" O GLU A1034 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N THR A1051 " --> pdb=" O ASN A1042 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY A1052 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU A1082 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N PHE A1054 " --> pdb=" O GLN A1080 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN A1080 " --> pdb=" O PHE A1054 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A1056 " --> pdb=" O ILE A1078 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.568A pdb=" N VAL A1105 " --> pdb=" O PHE A1121 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE A1121 " --> pdb=" O VAL A1105 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A1107 " --> pdb=" O VAL A1119 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A1117 " --> pdb=" O ASP A1109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1128 through 1134 removed outlier: 4.214A pdb=" N ASP A1130 " --> pdb=" O GLY A1141 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE A1147 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY A1151 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N SER A1161 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASP A1153 " --> pdb=" O MET A1159 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N MET A1159 " --> pdb=" O ASP A1153 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A1212 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A1164 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N HIS A1214 " --> pdb=" O ARG A1164 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS A1214 " --> pdb=" O LYS A1198 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS A1198 " --> pdb=" O HIS A1214 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR A1184 " --> pdb=" O PHE A1176 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE A1176 " --> pdb=" O TYR A1184 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA A1186 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A1174 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A1188 " --> pdb=" O MET A1172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 83 through 88 removed outlier: 5.340A pdb=" N PHE D 84 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 378 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 86 " --> pdb=" O PHE D 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AC6, first strand: chain 'D' and resid 138 through 143 removed outlier: 3.614A pdb=" N THR D 140 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 185 removed outlier: 4.362A pdb=" N SER D 196 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 201 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG D 213 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN D 205 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN D 211 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 224 through 227 removed outlier: 3.622A pdb=" N ILE D 234 " --> pdb=" O TRP D 246 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 269 removed outlier: 3.532A pdb=" N LYS D 266 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N CYS D 286 " --> pdb=" O CYS D 300 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS D 300 " --> pdb=" O CYS D 286 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 288 " --> pdb=" O LEU D 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 307 through 312 removed outlier: 6.768A pdb=" N ALA D 323 " --> pdb=" O MET D 308 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU D 310 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 321 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP D 312 " --> pdb=" O MET D 319 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N MET D 319 " --> pdb=" O TRP D 312 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS D 324 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER D 328 " --> pdb=" O CYS D 324 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.12 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4325 1.34 - 1.45: 2030 1.45 - 1.57: 7540 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 14006 Sorted by residual: bond pdb=" N ILE C 526 " pdb=" CA ILE C 526 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.27e-02 6.20e+03 7.68e+00 bond pdb=" N GLN C 527 " pdb=" CA GLN C 527 " ideal model delta sigma weight residual 1.457 1.489 -0.033 1.41e-02 5.03e+03 5.34e+00 bond pdb=" C ALA A 196 " pdb=" N PRO A 197 " ideal model delta sigma weight residual 1.330 1.355 -0.025 1.25e-02 6.40e+03 3.99e+00 bond pdb=" N LEU A 392 " pdb=" CA LEU A 392 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.56e-02 4.11e+03 3.42e+00 bond pdb=" N SER C 529 " pdb=" CA SER C 529 " ideal model delta sigma weight residual 1.462 1.487 -0.025 1.38e-02 5.25e+03 3.32e+00 ... (remaining 14001 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.35: 233 104.35 - 111.76: 6765 111.76 - 119.17: 4644 119.17 - 126.59: 7183 126.59 - 134.00: 194 Bond angle restraints: 19019 Sorted by residual: angle pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" C ILE A 511 " ideal model delta sigma weight residual 108.54 99.63 8.91 1.48e+00 4.57e-01 3.62e+01 angle pdb=" C ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta sigma weight residual 111.08 117.70 -6.62 1.17e+00 7.31e-01 3.20e+01 angle pdb=" N THR A 512 " pdb=" CA THR A 512 " pdb=" C THR A 512 " ideal model delta sigma weight residual 113.97 108.62 5.35 1.28e+00 6.10e-01 1.75e+01 angle pdb=" CA SER C 529 " pdb=" C SER C 529 " pdb=" O SER C 529 " ideal model delta sigma weight residual 122.13 118.03 4.10 1.13e+00 7.83e-01 1.32e+01 angle pdb=" CA PRO B 43 " pdb=" N PRO B 43 " pdb=" CD PRO B 43 " ideal model delta sigma weight residual 112.00 107.33 4.67 1.40e+00 5.10e-01 1.11e+01 ... (remaining 19014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 7284 17.47 - 34.95: 845 34.95 - 52.42: 238 52.42 - 69.89: 41 69.89 - 87.37: 11 Dihedral angle restraints: 8419 sinusoidal: 3284 harmonic: 5135 Sorted by residual: dihedral pdb=" CA TRP D 220 " pdb=" C TRP D 220 " pdb=" N ASP D 221 " pdb=" CA ASP D 221 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLU A1155 " pdb=" C GLU A1155 " pdb=" N PRO A1156 " pdb=" CA PRO A1156 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.65e+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 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 8416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1418 0.036 - 0.071: 489 0.071 - 0.107: 199 0.107 - 0.142: 75 0.142 - 0.178: 1 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CA ILE C 526 " pdb=" N ILE C 526 " pdb=" C ILE C 526 " pdb=" CB ILE C 526 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA ILE A 216 " pdb=" N ILE A 216 " pdb=" C ILE A 216 " pdb=" CB ILE A 216 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA GLU A1155 " pdb=" N GLU A1155 " pdb=" C GLU A1155 " pdb=" CB GLU A1155 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 2179 not shown) Planarity restraints: 2426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 390 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO D 391 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 391 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 391 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 384 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ASP D 384 " -0.024 2.00e-02 2.50e+03 pdb=" O ASP D 384 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO D 385 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 137 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C ASN A 137 " -0.024 2.00e-02 2.50e+03 pdb=" O ASN A 137 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP A 138 " 0.008 2.00e-02 2.50e+03 ... (remaining 2423 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 578 2.71 - 3.26: 13058 3.26 - 3.80: 23176 3.80 - 4.35: 30032 4.35 - 4.90: 50742 Nonbonded interactions: 117586 Sorted by model distance: nonbonded pdb=" N ASP A1296 " pdb=" OD1 ASP A1296 " model vdw 2.162 2.520 nonbonded pdb=" OH TYR A1266 " pdb=" O PRO A1306 " model vdw 2.197 2.440 nonbonded pdb=" OG SER A 520 " pdb=" OE1 GLU A 536 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR A 43 " pdb=" OD1 ASP A 45 " model vdw 2.223 2.440 nonbonded pdb=" O ILE A 511 " pdb=" OG SER A1225 " model vdw 2.230 2.440 ... (remaining 117581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.480 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 39.710 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 0.055 14006 Z= 0.178 Angle : 0.547 9.169 19019 Z= 0.298 Chirality : 0.045 0.178 2182 Planarity : 0.003 0.039 2426 Dihedral : 16.532 87.368 5087 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.25 % Allowed : 24.57 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1723 helix: -0.94 (0.49), residues: 112 sheet: 0.31 (0.22), residues: 567 loop : -1.37 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 312 HIS 0.003 0.001 HIS A 103 PHE 0.019 0.001 PHE C 555 TYR 0.024 0.001 TYR B 23 ARG 0.005 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 138 time to evaluate : 1.465 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 43 residues processed: 183 average time/residue: 0.8923 time to fit residues: 185.5339 Evaluate side-chains 173 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 40 residues processed: 3 average time/residue: 0.1694 time to fit residues: 2.8553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 376 GLN ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14006 Z= 0.281 Angle : 0.581 10.584 19019 Z= 0.307 Chirality : 0.048 0.199 2182 Planarity : 0.004 0.067 2426 Dihedral : 4.935 27.198 1874 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 6.62 % Allowed : 21.19 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1723 helix: -0.90 (0.48), residues: 119 sheet: -0.04 (0.21), residues: 586 loop : -1.39 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 204 HIS 0.004 0.001 HIS A 103 PHE 0.019 0.002 PHE C 555 TYR 0.016 0.001 TYR D 43 ARG 0.003 0.000 ARG A 963 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 140 time to evaluate : 1.695 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 54 residues processed: 215 average time/residue: 0.8857 time to fit residues: 218.6721 Evaluate side-chains 189 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 1.662 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 42 residues processed: 12 average time/residue: 0.3763 time to fit residues: 8.3094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 130 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 0.0050 chunk 126 optimal weight: 0.0670 overall best weight: 0.4132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 638 HIS A 700 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14006 Z= 0.145 Angle : 0.511 7.658 19019 Z= 0.268 Chirality : 0.046 0.157 2182 Planarity : 0.004 0.056 2426 Dihedral : 4.574 27.011 1874 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.03 % Allowed : 22.19 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1723 helix: -0.79 (0.48), residues: 120 sheet: -0.04 (0.21), residues: 580 loop : -1.30 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 312 HIS 0.004 0.001 HIS A 660 PHE 0.018 0.001 PHE C 555 TYR 0.015 0.001 TYR D 43 ARG 0.011 0.000 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 150 time to evaluate : 1.657 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 48 residues processed: 217 average time/residue: 0.8495 time to fit residues: 212.6467 Evaluate side-chains 183 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 135 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 41 residues processed: 7 average time/residue: 0.2769 time to fit residues: 4.6777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 700 ASN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN D 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14006 Z= 0.221 Angle : 0.537 9.688 19019 Z= 0.281 Chirality : 0.046 0.143 2182 Planarity : 0.004 0.042 2426 Dihedral : 4.739 27.175 1874 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.89 % Allowed : 22.91 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.19), residues: 1723 helix: -0.76 (0.48), residues: 120 sheet: -0.09 (0.21), residues: 581 loop : -1.33 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 312 HIS 0.003 0.001 HIS A 550 PHE 0.017 0.001 PHE C 555 TYR 0.020 0.001 TYR A1157 ARG 0.003 0.000 ARG A1341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 134 time to evaluate : 1.527 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 56 residues processed: 201 average time/residue: 0.8311 time to fit residues: 193.4873 Evaluate side-chains 183 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 127 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 46 residues processed: 10 average time/residue: 0.3533 time to fit residues: 6.9138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.0050 chunk 94 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 124 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14006 Z= 0.273 Angle : 0.563 10.836 19019 Z= 0.295 Chirality : 0.047 0.163 2182 Planarity : 0.004 0.034 2426 Dihedral : 4.946 27.728 1874 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 6.16 % Allowed : 22.78 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1723 helix: -0.76 (0.48), residues: 120 sheet: -0.13 (0.20), residues: 590 loop : -1.41 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 312 HIS 0.004 0.001 HIS A 550 PHE 0.017 0.002 PHE C 555 TYR 0.017 0.001 TYR D 43 ARG 0.002 0.000 ARG A1341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 136 time to evaluate : 1.691 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 55 residues processed: 205 average time/residue: 0.8195 time to fit residues: 194.7130 Evaluate side-chains 190 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 135 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 45 residues processed: 10 average time/residue: 0.3773 time to fit residues: 7.0655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 8.9990 chunk 150 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14006 Z= 0.310 Angle : 0.587 11.935 19019 Z= 0.306 Chirality : 0.048 0.219 2182 Planarity : 0.004 0.034 2426 Dihedral : 5.126 26.511 1874 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.63 % Allowed : 23.44 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1723 helix: -0.75 (0.48), residues: 120 sheet: -0.23 (0.20), residues: 598 loop : -1.46 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 312 HIS 0.004 0.001 HIS A 550 PHE 0.023 0.002 PHE C 555 TYR 0.017 0.002 TYR B 23 ARG 0.002 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 142 time to evaluate : 1.648 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 58 residues processed: 203 average time/residue: 0.8629 time to fit residues: 201.5096 Evaluate side-chains 189 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 48 residues processed: 10 average time/residue: 0.5042 time to fit residues: 8.4477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 729 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14006 Z= 0.227 Angle : 0.559 10.705 19019 Z= 0.291 Chirality : 0.047 0.212 2182 Planarity : 0.004 0.037 2426 Dihedral : 4.961 26.766 1874 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.10 % Allowed : 24.44 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1723 helix: -0.69 (0.48), residues: 120 sheet: -0.12 (0.21), residues: 584 loop : -1.43 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 312 HIS 0.004 0.001 HIS A 103 PHE 0.015 0.001 PHE A1218 TYR 0.019 0.001 TYR B 23 ARG 0.005 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 131 time to evaluate : 1.471 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 51 residues processed: 191 average time/residue: 0.8742 time to fit residues: 191.7033 Evaluate side-chains 179 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 44 residues processed: 7 average time/residue: 0.4329 time to fit residues: 6.0275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 38 ASN B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14006 Z= 0.192 Angle : 0.539 9.776 19019 Z= 0.279 Chirality : 0.047 0.246 2182 Planarity : 0.003 0.036 2426 Dihedral : 4.791 25.826 1874 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.77 % Allowed : 24.77 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 1723 helix: -0.64 (0.49), residues: 120 sheet: -0.14 (0.21), residues: 585 loop : -1.36 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 312 HIS 0.003 0.001 HIS A 550 PHE 0.014 0.001 PHE A1218 TYR 0.020 0.001 TYR B 23 ARG 0.004 0.000 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 127 time to evaluate : 1.730 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 55 residues processed: 186 average time/residue: 0.8287 time to fit residues: 179.0207 Evaluate side-chains 179 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 124 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 47 residues processed: 8 average time/residue: 0.4167 time to fit residues: 6.5016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 102 optimal weight: 0.0570 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14006 Z= 0.204 Angle : 0.544 9.524 19019 Z= 0.282 Chirality : 0.046 0.218 2182 Planarity : 0.004 0.036 2426 Dihedral : 4.794 25.892 1874 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.24 % Allowed : 25.76 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 1723 helix: -0.63 (0.49), residues: 120 sheet: -0.14 (0.21), residues: 585 loop : -1.35 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 312 HIS 0.003 0.001 HIS A 103 PHE 0.014 0.001 PHE A1218 TYR 0.022 0.001 TYR B 23 ARG 0.005 0.000 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 128 time to evaluate : 1.859 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 50 residues processed: 182 average time/residue: 0.8505 time to fit residues: 178.6008 Evaluate side-chains 176 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 126 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 45 residues processed: 5 average time/residue: 0.5823 time to fit residues: 5.7910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 38 ASN B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14006 Z= 0.236 Angle : 0.563 10.350 19019 Z= 0.291 Chirality : 0.047 0.214 2182 Planarity : 0.004 0.036 2426 Dihedral : 4.892 26.416 1874 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.97 % Allowed : 25.96 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1723 helix: -0.65 (0.48), residues: 120 sheet: -0.13 (0.21), residues: 590 loop : -1.39 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 312 HIS 0.004 0.001 HIS A 103 PHE 0.014 0.001 PHE A1218 TYR 0.024 0.001 TYR B 23 ARG 0.005 0.000 ARG A 674 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 126 time to evaluate : 2.147 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 48 residues processed: 179 average time/residue: 0.8757 time to fit residues: 180.4659 Evaluate side-chains 171 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.728 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 46 residues processed: 2 average time/residue: 0.2705 time to fit residues: 3.0176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.0060 chunk 137 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 38 ASN B 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102389 restraints weight = 23887.721| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.08 r_work: 0.3319 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14006 Z= 0.212 Angle : 0.552 10.160 19019 Z= 0.285 Chirality : 0.046 0.147 2182 Planarity : 0.004 0.036 2426 Dihedral : 4.835 26.598 1874 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.50 % Allowed : 25.43 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 1723 helix: -0.64 (0.49), residues: 120 sheet: -0.13 (0.21), residues: 592 loop : -1.38 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 312 HIS 0.004 0.001 HIS A 103 PHE 0.013 0.001 PHE A1218 TYR 0.023 0.001 TYR B 23 ARG 0.005 0.000 ARG A 674 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4423.58 seconds wall clock time: 80 minutes 28.95 seconds (4828.95 seconds total)