Starting phenix.real_space_refine on Sat Sep 12 06:53:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zgp_14710/09_2026/7zgp_14710.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 3 5.49 5 S 66 5.16 5 C 8967 2.51 5 N 2386 2.21 5 O 2631 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14055 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1236, 9718 Classifications: {'peptide': 1236} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 51, 'TRANS': 1184} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 81} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3128 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Classifications: {'DNA': 1, 'RNAv2': 3} Modifications used: {'rna2p_pur': 2} Link IDs: {'rna2p': 2, 'rna3p': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G:plan': 1, ' G:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10244 SG CYS B 67 38.875 29.498 27.651 1.00 63.63 S ATOM 10316 SG CYS B 75 38.302 29.737 31.418 1.00 63.85 S ATOM 10365 SG CYS B 81 37.962 26.335 29.637 1.00 79.00 S ATOM 9998 SG CYS B 34 55.409 11.914 39.472 1.00 87.77 S ATOM 10082 SG CYS B 46 54.053 11.738 43.101 1.00102.88 S ATOM 10125 SG CYS B 52 57.199 13.851 42.319 1.00 95.79 S Time building chain proxies: 2.92, per 1000 atoms: 0.21 Number of scatterers: 14055 At special positions: 0 Unit cell: (143.55, 115.5, 90.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 3 15.00 O 2631 8.00 N 2386 7.00 C 8967 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: 0.93 Conformation dependent library (CDL) restraints added in 753.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 56 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 46 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 52 " Number of angles added : 6 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 29 sheets defined 10.8% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.654A pdb=" N THR A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N THR A 242 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.530A pdb=" N ASN A 700 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 removed outlier: 4.573A pdb=" N SER A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 removed outlier: 3.735A pdb=" N SER A1206 " --> pdb=" O GLU A1203 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A1207 " --> pdb=" O PRO A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1203 through 1207' Processing helix chain 'A' and resid 1262 through 1280 Processing helix chain 'A' and resid 1287 through 1292 removed outlier: 3.511A pdb=" N ARG A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1318 removed outlier: 3.620A pdb=" N ARG A1315 " --> pdb=" O ASN A1311 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A1316 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS A1317 " --> pdb=" O ILE A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1329 Processing helix chain 'A' and resid 1334 through 1348 Processing helix chain 'A' and resid 1349 through 1355 removed outlier: 4.075A pdb=" N SER A1352 " --> pdb=" O SER A1349 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A1353 " --> pdb=" O MET A1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.692A pdb=" N ASN B 63 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.689A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.732A 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 79 removed outlier: 3.927A pdb=" N VAL D 77 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 402 through 407 Processing helix chain 'F' and resid 255 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 1224 through 1231 removed outlier: 7.542A pdb=" N PHE A1244 " --> pdb=" O PRO A1260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.512A pdb=" N LEU A 37 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU A 53 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL A 39 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 67 removed outlier: 7.940A pdb=" N SER A 74 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N PHE A 90 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 85 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 102 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 87 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 125 Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 218 removed outlier: 6.722A pdb=" N LEU A 230 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A 216 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 228 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A 218 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR A 226 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR A 248 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS A 275 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR A 250 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 273 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 252 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 281 through 286 removed outlier: 3.910A pdb=" N GLU A 298 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 310 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP A 303 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 327 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.927A pdb=" N THR A 343 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 363 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 388 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 410 removed outlier: 6.452A pdb=" N GLY A 425 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 408 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE A 423 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG A 410 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP A 421 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 503 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG A 435 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU A 501 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 517 removed outlier: 4.154A pdb=" N SER A 513 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 539 " --> pdb=" O ILE A 554 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 525 through 526 Processing sheet with id=AB2, first strand: chain 'A' and resid 561 through 567 removed outlier: 5.647A pdb=" N ILE A 562 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR A 915 " --> pdb=" O ILE A 562 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 564 " --> pdb=" O VAL A 913 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 578 removed outlier: 6.935A pdb=" N GLN A 573 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A 588 " --> pdb=" O GLN A 573 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TRP A 575 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU A 586 " --> pdb=" O TRP A 575 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 619 through 625 removed outlier: 4.119A pdb=" N HIS A 638 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 658 through 663 removed outlier: 3.671A pdb=" N HIS A 660 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 704 through 712 removed outlier: 4.779A pdb=" N ILE A 741 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 766 " --> pdb=" O ASN A 756 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU A 797 " --> pdb=" O LYS A 813 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 851 through 854 Processing sheet with id=AB8, first strand: chain 'A' and resid 944 through 950 removed outlier: 6.038A pdb=" N LEU A 944 " --> pdb=" O CYS A 961 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS A 961 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LYS A 946 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A 959 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A 991 " --> pdb=" O PHE A1009 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1014 through 1019 removed outlier: 5.183A pdb=" N VAL A1015 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA A1041 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY A1052 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A1082 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A1054 " --> pdb=" O GLN A1080 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A1080 " --> pdb=" O PHE A1054 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE A1056 " --> pdb=" O ILE A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1022 through 1023 Processing sheet with id=AC2, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.943A pdb=" N VAL A1105 " --> pdb=" O PHE A1121 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE A1121 " --> pdb=" O VAL A1105 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A1107 " --> pdb=" O VAL A1119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1128 through 1134 removed outlier: 4.377A pdb=" N ASP A1130 " --> pdb=" O GLY A1141 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE A1147 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A1151 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER A1161 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASP A1153 " --> pdb=" O MET A1159 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N MET A1159 " --> pdb=" O ASP A1153 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A1212 " --> pdb=" O LEU A1162 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A1164 " --> pdb=" O LEU A1212 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N HIS A1214 " --> pdb=" O ARG A1164 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS A1214 " --> pdb=" O LYS A1198 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYS A1198 " --> pdb=" O HIS A1214 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR A1184 " --> pdb=" O PHE A1176 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE A1176 " --> pdb=" O TYR A1184 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A1186 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A1174 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A1188 " --> pdb=" O MET A1172 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 81 through 88 removed outlier: 5.482A pdb=" N PHE D 84 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR D 378 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.158A pdb=" N ALA D 98 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 138 through 143 removed outlier: 3.505A pdb=" N THR D 140 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE D 159 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU D 171 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 161 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 185 removed outlier: 6.668A pdb=" N CYS D 195 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET D 183 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 193 " --> pdb=" O MET D 183 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE D 185 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS D 191 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN D 205 " --> pdb=" O GLN D 211 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLN D 211 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 222 through 227 removed outlier: 6.516A pdb=" N ALA D 237 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS D 225 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 235 " --> pdb=" O CYS D 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL D 243 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER D 256 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU D 245 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 264 through 268 removed outlier: 4.288A pdb=" N LYS D 266 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N CYS D 286 " --> pdb=" O CYS D 300 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS D 300 " --> pdb=" O CYS D 286 " (cutoff:3.500A) removed outlier: 6.458A 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: 6.967A pdb=" N ALA D 323 " --> pdb=" O MET D 308 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 310 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR D 321 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TRP D 312 " --> pdb=" O MET D 319 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET D 319 " --> pdb=" O TRP D 312 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N CYS D 324 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER D 328 " --> pdb=" O CYS D 324 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 209 through 210 removed outlier: 6.203A pdb=" N ARG F 209 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE F 241 " --> pdb=" O VAL F 248 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N PHE F 247 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE F 222 " --> pdb=" O PHE F 247 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4088 1.33 - 1.45: 2368 1.45 - 1.57: 7794 1.57 - 1.70: 6 1.70 - 1.82: 107 Bond restraints: 14363 Sorted by residual: bond pdb=" N VAL D 169 " pdb=" CA VAL D 169 " ideal model delta sigma weight residual 1.456 1.494 -0.038 9.50e-03 1.11e+04 1.58e+01 bond pdb=" N VAL A 703 " pdb=" CA VAL A 703 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.20e-02 6.94e+03 9.65e+00 bond pdb=" N VAL F 251 " pdb=" CA VAL F 251 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.14e-02 7.69e+03 8.34e+00 bond pdb=" N VAL A1255 " pdb=" CA VAL A1255 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.17e-02 7.31e+03 8.11e+00 bond pdb=" N ILE A 742 " pdb=" CA ILE A 742 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.15e-02 7.56e+03 7.99e+00 ... (remaining 14358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 19031 1.76 - 3.53: 408 3.53 - 5.29: 40 5.29 - 7.06: 5 7.06 - 8.82: 2 Bond angle restraints: 19486 Sorted by residual: angle pdb=" N PHE F 218 " pdb=" CA PHE F 218 " pdb=" C PHE F 218 " ideal model delta sigma weight residual 112.92 107.42 5.50 1.23e+00 6.61e-01 2.00e+01 angle pdb=" N PRO A1156 " pdb=" CA PRO A1156 " pdb=" C PRO A1156 " ideal model delta sigma weight residual 112.47 103.65 8.82 2.06e+00 2.36e-01 1.83e+01 angle pdb=" N ASP A 738 " pdb=" CA ASP A 738 " pdb=" C ASP A 738 " ideal model delta sigma weight residual 113.21 108.75 4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" CA ASP A1153 " pdb=" C ASP A1153 " pdb=" O ASP A1153 " ideal model delta sigma weight residual 121.68 117.53 4.15 1.18e+00 7.18e-01 1.24e+01 angle pdb=" CA ALA A1154 " pdb=" C ALA A1154 " pdb=" O ALA A1154 " ideal model delta sigma weight residual 119.68 117.24 2.44 7.10e-01 1.98e+00 1.18e+01 ... (remaining 19481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 7752 17.58 - 35.15: 687 35.15 - 52.73: 165 52.73 - 70.31: 36 70.31 - 87.88: 14 Dihedral angle restraints: 8654 sinusoidal: 3473 harmonic: 5181 Sorted by residual: dihedral pdb=" C4' A E 1 " pdb=" C3' A E 1 " pdb=" C2' A E 1 " pdb=" C1' A E 1 " ideal model delta sinusoidal sigma weight residual 36.34 -35.93 72.28 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" C2' A E 2 " pdb=" C1' A E 2 " ideal model delta sinusoidal sigma weight residual 36.34 -34.11 70.45 1 3.10e+00 1.04e-01 6.65e+02 dihedral pdb=" O4' A E 1 " pdb=" C4' A E 1 " pdb=" C3' A E 1 " pdb=" C2' A E 1 " ideal model delta sinusoidal sigma weight residual -35.15 25.52 -60.66 1 4.00e+00 6.25e-02 3.06e+02 ... (remaining 8651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1777 0.056 - 0.111: 373 0.111 - 0.167: 57 0.167 - 0.223: 8 0.223 - 0.279: 4 Chirality restraints: 2219 Sorted by residual: chirality pdb=" C2' A E 2 " pdb=" C3' A E 2 " pdb=" O2' A E 2 " pdb=" C1' A E 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C2' A E 1 " pdb=" C3' A E 1 " pdb=" O2' A E 1 " pdb=" C1' A E 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' A E 1 " pdb=" C4' A E 1 " pdb=" O3' A E 1 " pdb=" C2' A E 1 " both_signs ideal model delta sigma weight residual False -2.50 -2.74 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 2216 not shown) Planarity restraints: 2477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 390 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO D 391 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 391 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 391 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1065 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A1066 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1066 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1066 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 270 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO D 271 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 271 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 271 " -0.020 5.00e-02 4.00e+02 ... (remaining 2474 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 693 2.72 - 3.26: 13696 3.26 - 3.81: 24245 3.81 - 4.35: 32012 4.35 - 4.90: 53201 Nonbonded interactions: 123847 Sorted by model distance: nonbonded pdb=" N GLU B 35 " pdb=" OE1 GLU B 35 " model vdw 2.175 3.120 nonbonded pdb=" OG1 THR A1086 " pdb=" OG SER D 36 " model vdw 2.198 3.040 nonbonded pdb=" OG SER D 281 " pdb=" OD1 ASP D 283 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN A 756 " pdb=" OG SER A 768 " model vdw 2.206 3.040 nonbonded pdb=" N GLU A1264 " pdb=" OE1 GLU A1264 " model vdw 2.219 3.120 ... (remaining 123842 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: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.620 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 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 0.038 14371 Z= 0.213 Angle : 0.587 8.823 19492 Z= 0.348 Chirality : 0.049 0.279 2219 Planarity : 0.004 0.041 2477 Dihedral : 14.744 87.882 5294 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 0.96 % Allowed : 12.78 % Favored : 86.26 % 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 are not related in a simple way. whole: -0.84 (0.20), residues: 1743 helix: -0.05 (0.47), residues: 122 sheet: 0.27 (0.21), residues: 614 loop : -1.17 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 302 TYR 0.012 0.001 TYR D 347 PHE 0.020 0.001 PHE A1121 TRP 0.014 0.001 TRP D 312 HIS 0.002 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.21 (14363) covalent geometry : angle 0.58633 / 0.35 (19486) hydrogen bonds : bond 0.22892 / 15.47 ( 432) hydrogen bonds : angle 8.75272 / 6.01 ( 1119) metal coordination : bond 0.00684 / 0.35 ( 8) metal coordination : angle 1.08966 / 0.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.584 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: F 255 GLN cc_start: 0.7674 (tt0) cc_final: 0.7346 (tt0) outliers start: 15 outliers final: 8 residues processed: 151 average time/residue: 0.5703 time to fit residues: 95.4919 Evaluate side-chains 131 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN A 535 ASN B 21 GLN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.077410 restraints weight = 21059.294| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.89 r_work: 0.2844 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14371 Z= 0.199 Angle : 0.606 8.067 19492 Z= 0.323 Chirality : 0.051 0.728 2219 Planarity : 0.004 0.062 2477 Dihedral : 6.017 59.107 1946 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.88 % Favored : 93.06 % Rotamer: Outliers : 2.70 % Allowed : 12.65 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 1743 helix: -0.05 (0.46), residues: 130 sheet: 0.16 (0.20), residues: 623 loop : -1.23 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1232 TYR 0.015 0.001 TYR D 347 PHE 0.014 0.002 PHE D 320 TRP 0.014 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (14363) covalent geometry : angle 0.60510 / 0.32 (19486) hydrogen bonds : bond 0.05362 / 3.61 ( 432) hydrogen bonds : angle 6.45482 / 4.41 ( 1119) metal coordination : bond 0.01114 / 0.61 ( 8) metal coordination : angle 1.80086 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.603 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: D 168 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8313 (tmm) outliers start: 42 outliers final: 18 residues processed: 164 average time/residue: 0.5515 time to fit residues: 100.7620 Evaluate side-chains 143 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 729 GLN B 21 GLN F 255 GLN F 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.098093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080421 restraints weight = 20987.956| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.90 r_work: 0.2898 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14371 Z= 0.121 Angle : 0.537 6.941 19492 Z= 0.286 Chirality : 0.047 0.334 2219 Planarity : 0.004 0.040 2477 Dihedral : 5.803 59.082 1945 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.44 % Allowed : 14.26 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1743 helix: -0.06 (0.45), residues: 131 sheet: 0.07 (0.20), residues: 631 loop : -1.27 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1289 TYR 0.012 0.001 TYR A 642 PHE 0.014 0.001 PHE D 332 TRP 0.011 0.001 TRP D 312 HIS 0.002 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14363) covalent geometry : angle 0.53642 / 0.29 (19486) hydrogen bonds : bond 0.03965 / 2.68 ( 432) hydrogen bonds : angle 5.94570 / 4.05 ( 1119) metal coordination : bond 0.00557 / 0.30 ( 8) metal coordination : angle 1.46516 / 0.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.577 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: B 30 ASP cc_start: 0.8464 (m-30) cc_final: 0.8237 (m-30) REVERT: D 66 MET cc_start: 0.9160 (mmt) cc_final: 0.8697 (mmp) REVERT: D 182 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8245 (t0) REVERT: F 253 ASP cc_start: 0.8580 (t0) cc_final: 0.8352 (t0) outliers start: 38 outliers final: 19 residues processed: 160 average time/residue: 0.5449 time to fit residues: 97.3005 Evaluate side-chains 142 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain F residue 212 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079512 restraints weight = 21150.672| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.90 r_work: 0.2882 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 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 0.034 14371 Z= 0.143 Angle : 0.542 8.056 19492 Z= 0.288 Chirality : 0.047 0.299 2219 Planarity : 0.004 0.039 2477 Dihedral : 5.716 58.618 1943 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.76 % Allowed : 15.03 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1743 helix: 0.02 (0.45), residues: 131 sheet: -0.04 (0.20), residues: 627 loop : -1.29 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1289 TYR 0.013 0.001 TYR D 347 PHE 0.014 0.001 PHE D 320 TRP 0.012 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (14363) covalent geometry : angle 0.54184 / 0.29 (19486) hydrogen bonds : bond 0.03841 / 2.59 ( 432) hydrogen bonds : angle 5.77365 / 3.94 ( 1119) metal coordination : bond 0.00685 / 0.37 ( 8) metal coordination : angle 1.39997 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.607 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: B 30 ASP cc_start: 0.8481 (m-30) cc_final: 0.8260 (m-30) REVERT: D 182 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8424 (t0) REVERT: F 255 GLN cc_start: 0.8001 (tt0) cc_final: 0.7718 (tt0) outliers start: 43 outliers final: 19 residues processed: 164 average time/residue: 0.5529 time to fit residues: 100.8598 Evaluate side-chains 146 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 212 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.075380 restraints weight = 21257.026| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.90 r_work: 0.2808 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14371 Z= 0.277 Angle : 0.642 9.174 19492 Z= 0.339 Chirality : 0.051 0.399 2219 Planarity : 0.004 0.039 2477 Dihedral : 6.269 57.723 1943 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 2.50 % Allowed : 16.57 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.19), residues: 1743 helix: 0.01 (0.46), residues: 130 sheet: -0.18 (0.19), residues: 634 loop : -1.37 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1289 TYR 0.017 0.002 TYR D 347 PHE 0.015 0.002 PHE A1218 TRP 0.012 0.001 TRP D 312 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.28 (14363) covalent geometry : angle 0.64118 / 0.34 (19486) hydrogen bonds : bond 0.04584 / 3.07 ( 432) hydrogen bonds : angle 6.03312 / 4.14 ( 1119) metal coordination : bond 0.01502 / 0.85 ( 8) metal coordination : angle 1.40162 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.575 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: A 1121 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8695 (t80) REVERT: B 16 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: B 27 LEU cc_start: 0.9131 (mt) cc_final: 0.8895 (mp) outliers start: 39 outliers final: 21 residues processed: 148 average time/residue: 0.5233 time to fit residues: 86.1869 Evaluate side-chains 140 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 62 GLN F 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.079180 restraints weight = 20973.728| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.88 r_work: 0.2876 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14371 Z= 0.138 Angle : 0.544 7.317 19492 Z= 0.289 Chirality : 0.047 0.260 2219 Planarity : 0.004 0.040 2477 Dihedral : 5.954 67.758 1943 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.25 % Allowed : 16.70 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1743 helix: 0.10 (0.46), residues: 131 sheet: -0.15 (0.20), residues: 628 loop : -1.33 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1289 TYR 0.013 0.001 TYR D 347 PHE 0.014 0.001 PHE A1121 TRP 0.013 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (14363) covalent geometry : angle 0.54333 / 0.29 (19486) hydrogen bonds : bond 0.03662 / 2.47 ( 432) hydrogen bonds : angle 5.75359 / 3.92 ( 1119) metal coordination : bond 0.00551 / 0.29 ( 8) metal coordination : angle 1.29676 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.598 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. outliers start: 35 outliers final: 23 residues processed: 151 average time/residue: 0.5559 time to fit residues: 93.3790 Evaluate side-chains 144 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 216 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN B 21 GLN B 62 GLN F 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078506 restraints weight = 21182.178| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.89 r_work: 0.2863 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14371 Z= 0.160 Angle : 0.556 7.587 19492 Z= 0.294 Chirality : 0.047 0.270 2219 Planarity : 0.004 0.042 2477 Dihedral : 5.976 71.381 1943 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.44 % Allowed : 17.28 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1743 helix: 0.17 (0.47), residues: 124 sheet: -0.14 (0.20), residues: 626 loop : -1.31 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1289 TYR 0.013 0.001 TYR D 347 PHE 0.014 0.001 PHE A1121 TRP 0.012 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (14363) covalent geometry : angle 0.55518 / 0.29 (19486) hydrogen bonds : bond 0.03750 / 2.52 ( 432) hydrogen bonds : angle 5.74034 / 3.92 ( 1119) metal coordination : bond 0.00878 / 0.47 ( 8) metal coordination : angle 1.26993 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 0.495 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: B 92 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (mmm) outliers start: 38 outliers final: 27 residues processed: 152 average time/residue: 0.5242 time to fit residues: 88.8891 Evaluate side-chains 148 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 216 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN F 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.077568 restraints weight = 21041.722| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.88 r_work: 0.2847 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14371 Z= 0.184 Angle : 0.577 8.241 19492 Z= 0.304 Chirality : 0.048 0.292 2219 Planarity : 0.004 0.044 2477 Dihedral : 6.201 90.557 1943 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.31 % Allowed : 17.60 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1743 helix: 0.14 (0.47), residues: 124 sheet: -0.17 (0.20), residues: 626 loop : -1.33 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1289 TYR 0.015 0.001 TYR D 347 PHE 0.016 0.002 PHE D 320 TRP 0.012 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (14363) covalent geometry : angle 0.57722 / 0.30 (19486) hydrogen bonds : bond 0.03900 / 2.62 ( 432) hydrogen bonds : angle 5.77838 / 3.95 ( 1119) metal coordination : bond 0.00777 / 0.44 ( 8) metal coordination : angle 1.18001 / 0.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.457 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: B 48 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7886 (mtm-85) outliers start: 36 outliers final: 27 residues processed: 150 average time/residue: 0.4970 time to fit residues: 83.3358 Evaluate side-chains 146 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 174 optimal weight: 0.0170 chunk 9 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.095879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078088 restraints weight = 21055.069| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.88 r_work: 0.2857 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14371 Z= 0.165 Angle : 0.566 7.622 19492 Z= 0.299 Chirality : 0.047 0.278 2219 Planarity : 0.004 0.044 2477 Dihedral : 6.305 110.279 1943 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.12 % Allowed : 17.85 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1743 helix: 0.18 (0.47), residues: 124 sheet: -0.18 (0.20), residues: 626 loop : -1.32 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1289 TYR 0.014 0.001 TYR D 347 PHE 0.015 0.001 PHE D 320 TRP 0.013 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (14363) covalent geometry : angle 0.56553 / 0.30 (19486) hydrogen bonds : bond 0.03752 / 2.52 ( 432) hydrogen bonds : angle 5.73429 / 3.91 ( 1119) metal coordination : bond 0.00827 / 0.45 ( 8) metal coordination : angle 1.21800 / 0.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.450 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: B 21 GLN cc_start: 0.8821 (tt0) cc_final: 0.8427 (mt0) outliers start: 33 outliers final: 27 residues processed: 150 average time/residue: 0.5191 time to fit residues: 86.5003 Evaluate side-chains 148 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain F residue 216 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 55 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 73 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.079046 restraints weight = 21107.003| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.89 r_work: 0.2873 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14371 Z= 0.143 Angle : 0.552 7.350 19492 Z= 0.292 Chirality : 0.047 0.251 2219 Planarity : 0.004 0.045 2477 Dihedral : 6.321 122.340 1943 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.06 % Allowed : 18.05 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.19), residues: 1743 helix: 0.08 (0.46), residues: 130 sheet: -0.12 (0.20), residues: 618 loop : -1.32 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1289 TYR 0.012 0.001 TYR D 347 PHE 0.015 0.001 PHE F 247 TRP 0.013 0.001 TRP D 312 HIS 0.003 0.001 HIS D 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (14363) covalent geometry : angle 0.55215 / 0.29 (19486) hydrogen bonds : bond 0.03578 / 2.41 ( 432) hydrogen bonds : angle 5.66194 / 3.85 ( 1119) metal coordination : bond 0.00720 / 0.38 ( 8) metal coordination : angle 1.19002 / 0.58 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3486 Ramachandran restraints generated. 1743 Oldfield, 0 Emsley, 1743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.612 Fit side-chains TARDY: cannot create tardy model for: "ARG A1031 " (corrupted residue). Skipping it. REVERT: B 21 GLN cc_start: 0.8830 (tt0) cc_final: 0.8471 (mt0) REVERT: F 259 ASP cc_start: 0.8067 (m-30) cc_final: 0.7786 (m-30) outliers start: 32 outliers final: 27 residues processed: 153 average time/residue: 0.5346 time to fit residues: 91.0655 Evaluate side-chains 150 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1031 ARG Chi-restraints excluded: chain A residue 1032 LYS Chi-restraints excluded: chain A residue 1089 THR Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1170 GLN Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 171 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 114 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN F 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.081690 restraints weight = 20900.614| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.89 r_work: 0.2922 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14371 Z= 0.107 Angle : 0.521 7.773 19492 Z= 0.275 Chirality : 0.046 0.190 2219 Planarity : 0.004 0.045 2477 Dihedral : 6.112 125.429 1943 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.80 % Allowed : 18.56 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1743 helix: 0.24 (0.47), residues: 125 sheet: -0.06 (0.20), residues: 615 loop : -1.32 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1289 TYR 0.010 0.001 TYR D 43 PHE 0.015 0.001 PHE F 247 TRP 0.016 0.001 TRP D 312 HIS 0.002 0.000 HIS D 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14363) covalent geometry : angle 0.52090 / 0.28 (19486) hydrogen bonds : bond 0.03212 / 2.17 ( 432) hydrogen bonds : angle 5.48131 / 3.72 ( 1119) metal coordination : bond 0.00505 / 0.26 ( 8) metal coordination : angle 1.10058 / 0.51 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.51 seconds wall clock time: 69 minutes 44.17 seconds (4184.17 seconds total)