Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 11:59:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sv7_25445/04_2023/7sv7_25445_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6345 2.51 5 N 1585 2.21 5 O 1685 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9673 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9334 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 32, 'TRANS': 1140} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 254 Unusual residues: {' MG': 2, 'ATP': 2, 'C14': 1, 'CLR': 2, 'CV6': 1, 'D12': 4, 'DD9': 2, 'PJ8': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Time building chain proxies: 5.68, per 1000 atoms: 0.59 Number of scatterers: 9673 At special positions: 0 Unit cell: (81.37, 83.43, 145.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1685 8.00 N 1585 7.00 C 6345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 4 sheets defined 63.6% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 18 through 29 Proline residue: A 22 - end of helix removed outlier: 3.702A pdb=" N TYR A 28 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 29 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.696A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 removed outlier: 3.960A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.639A pdb=" N LEU A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 166 removed outlier: 3.688A pdb=" N ILE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.649A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 190 through 196 removed outlier: 3.762A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 216 removed outlier: 3.887A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.504A pdb=" N MET A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 267 removed outlier: 4.102A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 278 through 308 removed outlier: 4.089A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.819A pdb=" N GLY A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 316 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 317 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 320 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 323 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 4.033A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 4.462A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET A 348 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 465 through 472 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 527 through 532 removed outlier: 4.327A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 857 through 885 removed outlier: 4.062A pdb=" N PHE A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 removed outlier: 3.582A pdb=" N ALA A 923 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP A 924 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 957 removed outlier: 3.525A pdb=" N ILE A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 943 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.701A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 985 removed outlier: 4.143A pdb=" N ASP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1011 removed outlier: 3.565A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1060 Proline residue: A1021 - end of helix removed outlier: 3.618A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix Processing helix chain 'A' and resid 1062 through 1068 removed outlier: 3.524A pdb=" N ALA A1067 " --> pdb=" O TRP A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1121 removed outlier: 3.512A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A1116 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1117 " --> pdb=" O ALA A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1167 removed outlier: 3.783A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 4.039A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1285 removed outlier: 3.947A pdb=" N ALA A1285 " --> pdb=" O GLN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1322 removed outlier: 3.648A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1330 Processing helix chain 'A' and resid 1348 through 1361 Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 3.549A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.616A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1433 Processing helix chain 'A' and resid 1435 through 1440 removed outlier: 3.632A pdb=" N ALA A1440 " --> pdb=" O LEU A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1449 removed outlier: 3.558A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 Processing sheet with id= A, first strand: chain 'A' and resid 446 through 448 Processing sheet with id= B, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.654A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 615 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG A 600 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 456 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 602 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY A 458 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1232 through 1234 removed outlier: 3.705A pdb=" N MET A1210 " --> pdb=" O ILE A1234 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A1266 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1420 through 1424 removed outlier: 3.737A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLY A1244 " --> pdb=" O LEU A1399 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1365 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: 3.12 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2955 1.34 - 1.46: 1602 1.46 - 1.58: 5226 1.58 - 1.69: 10 1.69 - 1.81: 79 Bond restraints: 9872 Sorted by residual: bond pdb=" C15 CV6 A1515 " pdb=" N1 CV6 A1515 " ideal model delta sigma weight residual 1.473 1.352 0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" O5' ATP A1503 " pdb=" PA ATP A1503 " ideal model delta sigma weight residual 1.579 1.641 -0.062 1.10e-02 8.26e+03 3.17e+01 bond pdb=" O5' ATP A1504 " pdb=" PA ATP A1504 " ideal model delta sigma weight residual 1.579 1.638 -0.059 1.10e-02 8.26e+03 2.84e+01 bond pdb=" C5 CV6 A1515 " pdb=" C6 CV6 A1515 " ideal model delta sigma weight residual 1.375 1.444 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C8 CV6 A1515 " pdb=" N1 CV6 A1515 " ideal model delta sigma weight residual 1.478 1.416 0.062 2.00e-02 2.50e+03 9.56e+00 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 58.60 - 73.73: 6 73.73 - 88.87: 1 88.87 - 104.00: 118 104.00 - 119.14: 8135 119.14 - 134.27: 5088 Bond angle restraints: 13348 Sorted by residual: angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O2A ATP A1504 " ideal model delta sigma weight residual 114.42 72.44 41.98 3.53e+00 8.04e-02 1.42e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O5' ATP A1503 " ideal model delta sigma weight residual 110.65 69.89 40.76 3.49e+00 8.21e-02 1.36e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O2A ATP A1503 " ideal model delta sigma weight residual 114.42 74.33 40.09 3.53e+00 8.04e-02 1.29e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O5' ATP A1504 " ideal model delta sigma weight residual 110.65 71.66 38.99 3.49e+00 8.21e-02 1.25e+02 angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 130.34 9.53 1.00e+00 1.00e+00 9.09e+01 ... (remaining 13343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5440 18.00 - 36.00: 308 36.00 - 53.99: 60 53.99 - 71.99: 13 71.99 - 89.99: 7 Dihedral angle restraints: 5828 sinusoidal: 2372 harmonic: 3456 Sorted by residual: dihedral pdb=" CA LYS A 536 " pdb=" C LYS A 536 " pdb=" N ASP A 537 " pdb=" CA ASP A 537 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASN A1432 " pdb=" CB ASN A1432 " pdb=" CG ASN A1432 " pdb=" OD1 ASN A1432 " ideal model delta sinusoidal sigma weight residual 120.00 -173.28 -66.72 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" C18 CV6 A1515 " pdb=" C15 CV6 A1515 " pdb=" C16 CV6 A1515 " pdb=" N1 CV6 A1515 " ideal model delta sinusoidal sigma weight residual 38.25 122.68 -84.43 1 3.00e+01 1.11e-03 9.63e+00 ... (remaining 5825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 1535 0.175 - 0.350: 0 0.350 - 0.525: 0 0.525 - 0.700: 0 0.700 - 0.875: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C16 CV6 A1515 " pdb=" C15 CV6 A1515 " pdb=" C17 CV6 A1515 " pdb=" C19 CV6 A1515 " both_signs ideal model delta sigma weight residual True 2.52 1.64 0.88 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" CA ILE A 448 " pdb=" N ILE A 448 " pdb=" C ILE A 448 " pdb=" CB ILE A 448 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A1366 " pdb=" N ILE A1366 " pdb=" C ILE A1366 " pdb=" CB ILE A1366 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1533 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 CV6 A1515 " 0.072 2.00e-02 2.50e+03 1.16e-01 3.05e+02 pdb=" C19 CV6 A1515 " 0.028 2.00e-02 2.50e+03 pdb=" C20 CV6 A1515 " -0.094 2.00e-02 2.50e+03 pdb=" C21 CV6 A1515 " -0.187 2.00e-02 2.50e+03 pdb=" C22 CV6 A1515 " -0.156 2.00e-02 2.50e+03 pdb=" C23 CV6 A1515 " -0.022 2.00e-02 2.50e+03 pdb=" C24 CV6 A1515 " 0.069 2.00e-02 2.50e+03 pdb=" O4 CV6 A1515 " 0.126 2.00e-02 2.50e+03 pdb=" O5 CV6 A1515 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N CV6 A1515 " -0.026 2.00e-02 2.50e+03 6.31e-02 1.29e+02 pdb=" C1 CV6 A1515 " 0.155 2.00e-02 2.50e+03 pdb=" C10 CV6 A1515 " 0.015 2.00e-02 2.50e+03 pdb=" C11 CV6 A1515 " -0.026 2.00e-02 2.50e+03 pdb=" C12 CV6 A1515 " -0.108 2.00e-02 2.50e+03 pdb=" C4 CV6 A1515 " 0.001 2.00e-02 2.50e+03 pdb=" C5 CV6 A1515 " -0.033 2.00e-02 2.50e+03 pdb=" C6 CV6 A1515 " -0.042 2.00e-02 2.50e+03 pdb=" C7 CV6 A1515 " -0.041 2.00e-02 2.50e+03 pdb=" C8 CV6 A1515 " -0.005 2.00e-02 2.50e+03 pdb=" C9 CV6 A1515 " 0.032 2.00e-02 2.50e+03 pdb=" F CV6 A1515 " 0.093 2.00e-02 2.50e+03 pdb=" N1 CV6 A1515 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 CV6 A1515 " -0.003 2.00e-02 2.50e+03 1.35e-02 2.29e+00 pdb=" C16 CV6 A1515 " 0.011 2.00e-02 2.50e+03 pdb=" C8 CV6 A1515 " 0.016 2.00e-02 2.50e+03 pdb=" N1 CV6 A1515 " -0.023 2.00e-02 2.50e+03 pdb=" O3 CV6 A1515 " -0.002 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 18 2.58 - 3.16: 7940 3.16 - 3.74: 14217 3.74 - 4.32: 19714 4.32 - 4.90: 32766 Nonbonded interactions: 74655 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.003 2.170 nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 2.026 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.133 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.261 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.277 2.170 ... (remaining 74650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.150 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: 0.000 Extract box with map and model: 6.670 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.210 Find NCS groups from input model: 0.270 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.004 0.121 9872 Z= 0.213 Angle : 1.021 41.979 13348 Z= 0.408 Chirality : 0.044 0.875 1536 Planarity : 0.004 0.116 1608 Dihedral : 12.309 89.990 3592 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1163 helix: -0.21 (0.18), residues: 746 sheet: -1.41 (0.51), residues: 79 loop : -0.73 (0.33), residues: 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 218 time to evaluate : 1.119 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 223 average time/residue: 0.2589 time to fit residues: 80.5674 Evaluate side-chains 129 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0910 time to fit residues: 1.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 56 optimal weight: 0.0020 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 139 HIS A 268 ASN A 287 ASN A 290 GLN A 372 GLN A 376 GLN A 378 GLN A1035 GLN A1039 GLN A1054 HIS A1100 GLN A1148 ASN A1281 GLN A1412 GLN A1419 ASN A1432 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 9872 Z= 0.164 Angle : 0.531 7.119 13348 Z= 0.272 Chirality : 0.040 0.197 1536 Planarity : 0.003 0.029 1608 Dihedral : 6.663 97.812 1386 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1163 helix: 0.60 (0.19), residues: 745 sheet: -0.88 (0.59), residues: 69 loop : -0.63 (0.33), residues: 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.200 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 160 average time/residue: 0.2018 time to fit residues: 48.7006 Evaluate side-chains 126 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0984 time to fit residues: 2.8579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 207 GLN A1054 HIS A1411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 9872 Z= 0.161 Angle : 0.503 7.330 13348 Z= 0.255 Chirality : 0.040 0.180 1536 Planarity : 0.003 0.027 1608 Dihedral : 6.461 92.083 1386 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1163 helix: 0.78 (0.19), residues: 750 sheet: -0.86 (0.58), residues: 69 loop : -0.66 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.283 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 140 average time/residue: 0.1934 time to fit residues: 40.6275 Evaluate side-chains 128 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1015 time to fit residues: 3.8797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.0770 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 609 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9872 Z= 0.286 Angle : 0.584 8.067 13348 Z= 0.292 Chirality : 0.043 0.205 1536 Planarity : 0.004 0.032 1608 Dihedral : 6.954 91.835 1386 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1163 helix: 0.70 (0.19), residues: 750 sheet: -0.95 (0.55), residues: 69 loop : -0.73 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.068 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 137 average time/residue: 0.1980 time to fit residues: 40.8450 Evaluate side-chains 127 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0959 time to fit residues: 3.5648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 102 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A1054 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9872 Z= 0.149 Angle : 0.492 8.137 13348 Z= 0.248 Chirality : 0.040 0.314 1536 Planarity : 0.003 0.029 1608 Dihedral : 6.664 89.254 1386 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1163 helix: 0.93 (0.19), residues: 752 sheet: -0.97 (0.55), residues: 70 loop : -0.64 (0.33), residues: 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.178 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 138 average time/residue: 0.1962 time to fit residues: 40.6678 Evaluate side-chains 127 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1000 time to fit residues: 2.9256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 220 GLN A1054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9872 Z= 0.215 Angle : 0.533 7.712 13348 Z= 0.266 Chirality : 0.041 0.205 1536 Planarity : 0.003 0.031 1608 Dihedral : 6.757 89.256 1386 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1163 helix: 1.00 (0.19), residues: 740 sheet: -0.59 (0.60), residues: 60 loop : -0.63 (0.32), residues: 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.131 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 138 average time/residue: 0.1917 time to fit residues: 40.0279 Evaluate side-chains 128 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1008 time to fit residues: 3.4714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9872 Z= 0.146 Angle : 0.505 9.529 13348 Z= 0.251 Chirality : 0.039 0.217 1536 Planarity : 0.003 0.029 1608 Dihedral : 6.545 87.348 1386 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1163 helix: 1.12 (0.19), residues: 746 sheet: -0.59 (0.59), residues: 60 loop : -0.62 (0.32), residues: 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.202 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 137 average time/residue: 0.1978 time to fit residues: 40.7534 Evaluate side-chains 124 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1023 time to fit residues: 2.4633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 0.0070 chunk 103 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 9872 Z= 0.145 Angle : 0.498 8.530 13348 Z= 0.250 Chirality : 0.039 0.191 1536 Planarity : 0.003 0.030 1608 Dihedral : 6.388 85.867 1386 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1163 helix: 1.26 (0.19), residues: 740 sheet: -0.51 (0.60), residues: 60 loop : -0.55 (0.32), residues: 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 1.053 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 139 average time/residue: 0.1951 time to fit residues: 40.8590 Evaluate side-chains 122 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1120 time to fit residues: 2.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 538 ASN A 958 GLN A1411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 9872 Z= 0.146 Angle : 0.501 8.725 13348 Z= 0.251 Chirality : 0.039 0.177 1536 Planarity : 0.003 0.029 1608 Dihedral : 6.324 85.095 1386 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1163 helix: 1.35 (0.20), residues: 738 sheet: -0.26 (0.70), residues: 50 loop : -0.54 (0.32), residues: 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.289 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 133 average time/residue: 0.2067 time to fit residues: 41.0442 Evaluate side-chains 124 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0943 time to fit residues: 1.9252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.0970 chunk 53 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 108 optimal weight: 0.0570 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 9872 Z= 0.146 Angle : 0.504 8.462 13348 Z= 0.252 Chirality : 0.039 0.169 1536 Planarity : 0.003 0.040 1608 Dihedral : 6.264 86.524 1386 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1163 helix: 1.40 (0.19), residues: 738 sheet: -0.52 (0.59), residues: 60 loop : -0.54 (0.32), residues: 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.257 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2026 time to fit residues: 37.6453 Evaluate side-chains 120 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.105 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 958 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121194 restraints weight = 14271.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124432 restraints weight = 7570.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127102 restraints weight = 4431.824| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 9872 Z= 0.142 Angle : 0.496 8.280 13348 Z= 0.247 Chirality : 0.039 0.298 1536 Planarity : 0.003 0.056 1608 Dihedral : 6.237 87.458 1386 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1163 helix: 1.44 (0.19), residues: 738 sheet: -0.50 (0.58), residues: 65 loop : -0.53 (0.32), residues: 360 =============================================================================== Job complete usr+sys time: 1857.36 seconds wall clock time: 34 minutes 53.65 seconds (2093.65 seconds total)