Starting phenix.real_space_refine on Thu Sep 18 03:46:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zgq_14711/09_2025/7zgq_14711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgq_14711/09_2025/7zgq_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/cci-nas-00/data/ceres_data/7zgq_14711/09_2025/7zgq_14711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgq_14711/09_2025/7zgq_14711.map" model { file = "/net/cci-nas-00/data/ceres_data/7zgq_14711/09_2025/7zgq_14711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgq_14711/09_2025/7zgq_14711.cif" } resolution = 2.8 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: 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 5, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 12, 'ASN:plan1': 2, 'GLN:plan1': 1} 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: {'GLU:plan': 3, 'PHE:plan': 1, '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, 'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 4, 'TRP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 58 Time building chain proxies: 3.16, per 1000 atoms: 0.23 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 - 3.00 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: 1.08 Conformation dependent library (CDL) restraints added in 628.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.68 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: 3.07 Time building geometry restraints manager: 1.48 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: 0.00 - 1.83: 18745 1.83 - 3.67: 229 3.67 - 5.50: 35 5.50 - 7.34: 5 7.34 - 9.17: 5 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 3.120 nonbonded pdb=" OH TYR A1266 " pdb=" O PRO A1306 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 520 " pdb=" OE1 GLU A 536 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 43 " pdb=" OD1 ASP A 45 " model vdw 2.223 3.040 nonbonded pdb=" O ILE A 511 " pdb=" OG SER A1225 " model vdw 2.230 3.040 ... (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 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- 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= 0.128 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 : 11.31 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A 612 TYR 0.024 0.001 TYR B 23 PHE 0.019 0.001 PHE C 555 TRP 0.012 0.001 TRP D 312 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00271 (14006) covalent geometry : angle 0.54675 (19019) hydrogen bonds : bond 0.25425 ( 405) hydrogen bonds : angle 9.11745 ( 1044) *********************** 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 to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.517 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: 0.4506 time to fit residues: 93.1752 Evaluate side-chains 173 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1158 ARG Chi-restraints excluded: chain A residue 1160 ILE Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1296 ASP Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 397 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 608 HIS A 740 GLN A 788 ASN A1012 ASN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN D 188 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101397 restraints weight = 24232.427| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.11 r_work: 0.3304 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14006 Z= 0.175 Angle : 0.586 10.853 19019 Z= 0.312 Chirality : 0.048 0.190 2182 Planarity : 0.004 0.069 2426 Dihedral : 6.854 52.206 1941 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.50 % Allowed : 21.79 % Favored : 72.72 % 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 aren not related in a simple way. whole: -1.23 (0.20), residues: 1723 helix: -1.03 (0.47), residues: 124 sheet: -0.04 (0.21), residues: 584 loop : -1.28 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 963 TYR 0.016 0.001 TYR D 43 PHE 0.016 0.001 PHE C 555 TRP 0.011 0.001 TRP D 162 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00390 (14006) covalent geometry : angle 0.58645 (19019) hydrogen bonds : bond 0.04953 ( 405) hydrogen bonds : angle 6.66595 ( 1044) *********************** 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 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 146 time to evaluate : 0.368 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: B 22 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: D 170 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7604 (tmtm) REVERT: D 221 ASP cc_start: 0.7071 (t0) cc_final: 0.6866 (t0) outliers start: 83 outliers final: 40 residues processed: 204 average time/residue: 0.3983 time to fit residues: 92.5396 Evaluate side-chains 175 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 788 ASN 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 1004 ILE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1296 ASP Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 262 HIS Chi-restraints excluded: chain D residue 293 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 147 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 81 optimal weight: 0.0060 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.3176 ------------------------------------------------------------------------------- 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 788 ASN A1012 ASN B 62 GLN D 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.120887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101604 restraints weight = 24309.073| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.11 r_work: 0.3308 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14006 Z= 0.154 Angle : 0.560 10.923 19019 Z= 0.296 Chirality : 0.047 0.158 2182 Planarity : 0.004 0.053 2426 Dihedral : 6.434 55.751 1910 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.30 % Allowed : 22.12 % Favored : 72.58 % 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 aren not related in a simple way. whole: -1.26 (0.19), residues: 1723 helix: -1.01 (0.47), residues: 125 sheet: -0.10 (0.21), residues: 582 loop : -1.28 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 674 TYR 0.016 0.001 TYR D 43 PHE 0.018 0.001 PHE C 555 TRP 0.011 0.001 TRP D 312 HIS 0.003 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00345 (14006) covalent geometry : angle 0.56049 (19019) hydrogen bonds : bond 0.04407 ( 405) hydrogen bonds : angle 6.35679 ( 1044) *********************** 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 218 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 138 time to evaluate : 0.471 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: A 298 GLU cc_start: 0.7173 (mp0) cc_final: 0.6950 (mp0) REVERT: A 646 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8274 (t80) REVERT: A 656 TYR cc_start: 0.7626 (m-10) cc_final: 0.7296 (m-10) REVERT: A 727 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6232 (tm-30) REVERT: B 22 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6818 (mt-10) REVERT: D 170 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7602 (tttm) REVERT: D 295 MET cc_start: 0.8768 (mmm) cc_final: 0.8562 (mmp) REVERT: D 383 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.6992 (pp) outliers start: 80 outliers final: 37 residues processed: 192 average time/residue: 0.4008 time to fit residues: 88.1487 Evaluate side-chains 176 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 943 THR 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 1048 THR Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN D 100 GLN D 188 ASN D 211 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.121002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.101748 restraints weight = 24168.157| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.10 r_work: 0.3311 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14006 Z= 0.148 Angle : 0.547 11.419 19019 Z= 0.288 Chirality : 0.047 0.146 2182 Planarity : 0.004 0.042 2426 Dihedral : 6.225 58.999 1905 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.43 % Allowed : 22.58 % Favored : 71.99 % 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 aren not related in a simple way. whole: -1.29 (0.19), residues: 1723 helix: -0.76 (0.48), residues: 119 sheet: -0.19 (0.20), residues: 588 loop : -1.30 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.016 0.001 TYR D 43 PHE 0.014 0.001 PHE A1218 TRP 0.011 0.001 TRP D 312 HIS 0.003 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00335 (14006) covalent geometry : angle 0.54654 (19019) hydrogen bonds : bond 0.04077 ( 405) hydrogen bonds : angle 6.11220 ( 1044) *********************** 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 229 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 147 time to evaluate : 0.584 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 125 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7969 (mmm) REVERT: A 656 TYR cc_start: 0.7546 (m-10) cc_final: 0.6717 (m-10) REVERT: A 727 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: B 22 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: D 170 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7582 (tttm) REVERT: D 211 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7330 (tp-100) REVERT: D 295 MET cc_start: 0.8692 (mmm) cc_final: 0.8474 (mmp) REVERT: D 383 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7004 (pp) outliers start: 82 outliers final: 40 residues processed: 203 average time/residue: 0.3930 time to fit residues: 91.5349 Evaluate side-chains 178 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1305 ARG Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 253 CYS Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 154 optimal weight: 0.0980 chunk 163 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 232 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN D 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102517 restraints weight = 24298.620| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.11 r_work: 0.3325 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1248 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= 0.129 Angle : 0.539 10.976 19019 Z= 0.282 Chirality : 0.046 0.144 2182 Planarity : 0.004 0.042 2426 Dihedral : 5.993 52.454 1901 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.10 % Allowed : 22.91 % Favored : 71.99 % 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 aren not related in a simple way. whole: -1.24 (0.20), residues: 1723 helix: -0.90 (0.47), residues: 125 sheet: -0.12 (0.21), residues: 583 loop : -1.25 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.023 0.001 TYR A1157 PHE 0.013 0.001 PHE D 332 TRP 0.011 0.001 TRP D 312 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00291 (14006) covalent geometry : angle 0.53913 (19019) hydrogen bonds : bond 0.03816 ( 405) hydrogen bonds : angle 5.99237 ( 1044) *********************** 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 210 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 133 time to evaluate : 0.566 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 125 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7984 (mmm) REVERT: A 198 SER cc_start: 0.7458 (m) cc_final: 0.7236 (p) REVERT: A 598 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7746 (tp) REVERT: A 727 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6295 (tm-30) REVERT: B 22 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: D 131 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7915 (ttm) REVERT: D 170 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7638 (tttm) REVERT: D 383 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.6916 (pp) outliers start: 77 outliers final: 45 residues processed: 186 average time/residue: 0.4133 time to fit residues: 87.6191 Evaluate side-chains 181 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 727 GLU 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 1003 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1098 MET Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain A residue 1305 ARG Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 26 optimal weight: 0.0170 chunk 11 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103378 restraints weight = 24187.326| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.09 r_work: 0.3337 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1319 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= 0.119 Angle : 0.525 10.170 19019 Z= 0.275 Chirality : 0.046 0.143 2182 Planarity : 0.003 0.043 2426 Dihedral : 5.772 50.804 1900 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.70 % Allowed : 23.58 % Favored : 71.72 % 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 aren not related in a simple way. whole: -1.24 (0.20), residues: 1723 helix: -0.65 (0.49), residues: 119 sheet: -0.14 (0.20), residues: 583 loop : -1.27 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 674 TYR 0.015 0.001 TYR D 43 PHE 0.013 0.001 PHE D 332 TRP 0.011 0.001 TRP D 312 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00268 (14006) covalent geometry : angle 0.52479 (19019) hydrogen bonds : bond 0.03628 ( 405) hydrogen bonds : angle 5.88174 ( 1044) *********************** 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 213 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 0.570 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 598 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7735 (tp) REVERT: A 676 ASP cc_start: 0.8039 (m-30) cc_final: 0.7748 (m-30) REVERT: A 727 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: B 22 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: D 131 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7924 (ttm) REVERT: D 221 ASP cc_start: 0.7125 (t70) cc_final: 0.6903 (t70) REVERT: D 383 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.7008 (pp) outliers start: 71 outliers final: 39 residues processed: 189 average time/residue: 0.3981 time to fit residues: 86.2880 Evaluate side-chains 172 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1098 MET Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 142 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN B 62 GLN D 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102599 restraints weight = 24255.243| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.10 r_work: 0.3326 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14006 Z= 0.138 Angle : 0.544 10.833 19019 Z= 0.283 Chirality : 0.046 0.148 2182 Planarity : 0.004 0.043 2426 Dihedral : 5.765 50.785 1897 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.23 % Allowed : 23.31 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.20), residues: 1723 helix: -0.64 (0.49), residues: 119 sheet: -0.16 (0.20), residues: 584 loop : -1.29 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 612 TYR 0.018 0.001 TYR B 23 PHE 0.013 0.001 PHE D 332 TRP 0.010 0.001 TRP D 312 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00314 (14006) covalent geometry : angle 0.54359 (19019) hydrogen bonds : bond 0.03754 ( 405) hydrogen bonds : angle 5.87575 ( 1044) *********************** 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 207 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 128 time to evaluate : 0.517 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 544 ILE cc_start: 0.8678 (mm) cc_final: 0.8456 (tp) REVERT: A 125 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7989 (mmm) REVERT: A 598 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7714 (tp) REVERT: A 727 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6288 (tm-30) REVERT: A 909 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7822 (mmpt) REVERT: B 22 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6808 (mt-10) REVERT: D 136 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 221 ASP cc_start: 0.7111 (t70) cc_final: 0.6825 (t70) REVERT: D 383 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7076 (pp) outliers start: 79 outliers final: 40 residues processed: 186 average time/residue: 0.3986 time to fit residues: 85.0743 Evaluate side-chains 172 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 727 GLU 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 1003 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1098 MET Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 0.0570 chunk 150 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 123 optimal weight: 0.0870 chunk 104 optimal weight: 0.6980 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 660 HIS A 788 ASN A1012 ASN B 62 GLN D 211 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.124500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105579 restraints weight = 24056.265| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.09 r_work: 0.3373 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14006 Z= 0.096 Angle : 0.519 9.023 19019 Z= 0.269 Chirality : 0.046 0.143 2182 Planarity : 0.003 0.043 2426 Dihedral : 5.468 50.483 1895 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.17 % Allowed : 24.57 % Favored : 71.26 % 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 aren not related in a simple way. whole: -1.22 (0.20), residues: 1723 helix: -0.54 (0.49), residues: 118 sheet: -0.22 (0.20), residues: 593 loop : -1.22 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 674 TYR 0.021 0.001 TYR B 23 PHE 0.014 0.001 PHE D 332 TRP 0.012 0.001 TRP D 312 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00216 (14006) covalent geometry : angle 0.51896 (19019) hydrogen bonds : bond 0.03251 ( 405) hydrogen bonds : angle 5.71126 ( 1044) *********************** 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 208 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 0.576 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 198 SER cc_start: 0.7225 (p) cc_final: 0.6988 (m) REVERT: A 598 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7764 (tp) REVERT: A 909 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7816 (mmpt) REVERT: A 1025 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7417 (mm) REVERT: A 1159 MET cc_start: 0.8653 (mmm) cc_final: 0.8405 (mtp) REVERT: D 131 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (ttm) REVERT: D 136 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8226 (p) REVERT: D 231 MET cc_start: 0.7462 (mtm) cc_final: 0.7192 (ptp) REVERT: D 383 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7057 (pp) outliers start: 63 outliers final: 35 residues processed: 190 average time/residue: 0.4178 time to fit residues: 90.4390 Evaluate side-chains 167 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 788 ASN 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 1003 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1016 ASN Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1098 MET Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 ASN ** A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN D 188 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.118711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099302 restraints weight = 24420.331| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.10 r_work: 0.3270 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 14006 Z= 0.255 Angle : 0.658 14.423 19019 Z= 0.340 Chirality : 0.050 0.153 2182 Planarity : 0.004 0.043 2426 Dihedral : 6.169 50.088 1892 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.91 % Allowed : 24.30 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -1.38 (0.19), residues: 1723 helix: -0.82 (0.47), residues: 119 sheet: -0.28 (0.20), residues: 612 loop : -1.36 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 674 TYR 0.021 0.002 TYR B 23 PHE 0.017 0.002 PHE A1185 TRP 0.008 0.002 TRP D 312 HIS 0.007 0.001 HIS A1195 Details of bonding type rmsd covalent geometry : bond 0.00588 (14006) covalent geometry : angle 0.65827 (19019) hydrogen bonds : bond 0.04621 ( 405) hydrogen bonds : angle 6.14181 ( 1044) *********************** 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 191 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 0.401 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 598 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7679 (tp) REVERT: A 909 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7862 (mmpt) REVERT: A 1159 MET cc_start: 0.8687 (mmm) cc_final: 0.8467 (mtp) REVERT: D 383 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7237 (pp) outliers start: 59 outliers final: 41 residues processed: 178 average time/residue: 0.4270 time to fit residues: 86.6933 Evaluate side-chains 171 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 700 ASN 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 1003 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1098 MET Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1203 GLU Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 18 optimal weight: 0.0000 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 overall best weight: 0.5162 ------------------------------------------------------------------------------- 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 788 ASN A1012 ASN A1042 ASN B 62 GLN D 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104076 restraints weight = 24042.660| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.09 r_work: 0.3350 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1556 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= 0.108 Angle : 0.553 11.792 19019 Z= 0.283 Chirality : 0.047 0.217 2182 Planarity : 0.004 0.042 2426 Dihedral : 5.648 50.245 1891 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.11 % Allowed : 25.63 % Favored : 71.26 % 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 aren not related in a simple way. whole: -1.27 (0.20), residues: 1723 helix: -0.53 (0.50), residues: 113 sheet: -0.26 (0.20), residues: 590 loop : -1.25 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 612 TYR 0.023 0.001 TYR A 656 PHE 0.016 0.001 PHE C 555 TRP 0.013 0.001 TRP D 312 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00246 (14006) covalent geometry : angle 0.55255 (19019) hydrogen bonds : bond 0.03454 ( 405) hydrogen bonds : angle 5.86793 ( 1044) ********************** 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 177 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.621 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 198 SER cc_start: 0.7221 (p) cc_final: 0.6970 (m) REVERT: A 598 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7698 (tp) REVERT: A 909 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7879 (mmpt) REVERT: D 136 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8160 (p) REVERT: D 383 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7097 (pp) outliers start: 47 outliers final: 35 residues processed: 167 average time/residue: 0.4076 time to fit residues: 77.6150 Evaluate side-chains 164 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 646 PHE Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 788 ASN 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 1003 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1048 THR Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1093 VAL Chi-restraints excluded: chain A residue 1098 MET Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1241 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 293 TYR Chi-restraints excluded: chain D residue 383 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 153 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 163 optimal weight: 0.0570 chunk 30 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- 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** A1012 ASN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104035 restraints weight = 24266.175| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.09 r_work: 0.3349 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 14006 Z= 0.170 Angle : 0.784 59.199 19019 Z= 0.452 Chirality : 0.050 0.858 2182 Planarity : 0.004 0.056 2426 Dihedral : 5.600 50.155 1889 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.78 % Allowed : 25.89 % Favored : 71.32 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: -1.27 (0.20), residues: 1723 helix: -0.53 (0.50), residues: 113 sheet: -0.26 (0.20), residues: 590 loop : -1.25 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 612 TYR 0.020 0.001 TYR A 656 PHE 0.014 0.001 PHE D 332 TRP 0.013 0.001 TRP D 312 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00328 (14006) covalent geometry : angle 0.78383 (19019) hydrogen bonds : bond 0.03461 ( 405) hydrogen bonds : angle 5.86615 ( 1044) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.92 seconds wall clock time: 75 minutes 39.65 seconds (4539.65 seconds total)