Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 20:22:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/04_2023/6urg_20860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/04_2023/6urg_20860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/04_2023/6urg_20860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/04_2023/6urg_20860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/04_2023/6urg_20860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/04_2023/6urg_20860.pdb" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 82 5.16 5 C 8458 2.51 5 N 2291 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 702": "NH1" <-> "NH2" Residue "A PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "F PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13214 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1202, 9532 Classifications: {'peptide': 1202} Link IDs: {'PTRANS': 66, 'TRANS': 1135} Chain breaks: 9 Chain: "B" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2953 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 452 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "F" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 276 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12791 SG CYS C 41 63.781 36.183 15.874 1.00 39.96 S ATOM 12890 SG CYS C 55 66.450 34.788 19.578 1.00 39.96 S Time building chain proxies: 6.95, per 1000 atoms: 0.53 Number of scatterers: 13214 At special positions: 0 Unit cell: (87.98, 135.68, 102.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 82 16.00 O 2382 8.00 N 2291 7.00 C 8458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 59 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 41 " 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3106 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 31 sheets defined 6.8% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1153 through 1156 removed outlier: 3.620A pdb=" N THR A1156 " --> pdb=" O GLN A1153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1156' Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.526A pdb=" N LEU A1359 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 Processing helix chain 'A' and resid 1377 through 1383 Processing helix chain 'A' and resid 1403 through 1407 Processing helix chain 'A' and resid 1411 through 1422 removed outlier: 3.681A pdb=" N SER A1416 " --> pdb=" O THR A1412 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A1417 " --> pdb=" O MET A1413 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A1419 " --> pdb=" O ARG A1415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A1422 " --> pdb=" O LEU A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1434 removed outlier: 3.769A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1439 removed outlier: 3.626A pdb=" N VAL A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 73 removed outlier: 3.849A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 4.053A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.682A pdb=" N ASN B 104 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 106 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 removed outlier: 3.501A pdb=" N VAL C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 1312 through 1315 removed outlier: 7.087A pdb=" N HIS A1334 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 4.170A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ARG A 42 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 68 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN A 44 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU A 66 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 84 removed outlier: 6.688A pdb=" N SER A 97 " --> pdb=" O MET A 79 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET A 81 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 95 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 83 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA A 93 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.851A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 260 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 242 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER A 244 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 254 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.103A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 330 removed outlier: 3.879A pdb=" N LYS A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.684A pdb=" N ASP A 467 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS A 395 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL A 465 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR A 397 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE A 463 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.277A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER A 974 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 538 removed outlier: 3.740A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.557A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 612 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 617 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A 620 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS A 636 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 651 removed outlier: 7.504A pdb=" N MET A 659 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N CYS A 649 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 657 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR A 655 " --> pdb=" O VAL A 651 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 695 through 703 removed outlier: 3.507A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 782 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG A 803 " --> pdb=" O GLN A 798 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.521A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE A 873 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 865 " --> pdb=" O LEU A 872 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 817 through 818 removed outlier: 3.521A pdb=" N PHE A 892 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.883A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1024 through 1028 removed outlier: 3.717A pdb=" N TYR A1024 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1046 through 1048 Processing sheet with id=AC2, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.665A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A1159 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1172 through 1178 removed outlier: 4.036A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A1190 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE A1205 " --> pdb=" O ILE A1190 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.615A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A1231 " --> pdb=" O ARG A1248 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ARG A1248 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A1233 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A1237 " --> pdb=" O THR A1242 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A1242 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.970A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.970A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.574A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 380 " --> pdb=" O GLY B 393 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 122 through 127 removed outlier: 7.004A pdb=" N GLY B 137 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N VAL B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL B 135 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP B 127 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG B 133 " --> pdb=" O TRP B 127 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 168 through 169 removed outlier: 4.834A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.944A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 226 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE B 239 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 228 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AD3, first strand: chain 'B' and resid 291 through 296 removed outlier: 3.630A pdb=" N GLU B 293 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 334 through 339 342 hydrogen bonds defined for protein. 906 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: 5.83 Time building geometry restraints manager: 5.65 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: 3470 1.33 - 1.45: 2468 1.45 - 1.57: 7464 1.57 - 1.69: 1 1.69 - 1.81: 133 Bond restraints: 13536 Sorted by residual: bond pdb=" CA TYR A 213 " pdb=" C TYR A 213 " ideal model delta sigma weight residual 1.523 1.575 -0.052 1.34e-02 5.57e+03 1.52e+01 bond pdb=" N TYR A 213 " pdb=" CA TYR A 213 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.42e+00 bond pdb=" N LEU A 845 " pdb=" CA LEU A 845 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.30e+00 bond pdb=" CA THR A 216 " pdb=" C THR A 216 " ideal model delta sigma weight residual 1.521 1.496 0.026 1.19e-02 7.06e+03 4.65e+00 bond pdb=" C TYR A 108 " pdb=" N ASP A 109 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.44e-02 4.82e+03 4.13e+00 ... (remaining 13531 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.34: 258 104.34 - 111.77: 6271 111.77 - 119.20: 4701 119.20 - 126.63: 6877 126.63 - 134.06: 254 Bond angle restraints: 18361 Sorted by residual: angle pdb=" N LEU B 386 " pdb=" CA LEU B 386 " pdb=" C LEU B 386 " ideal model delta sigma weight residual 109.46 98.52 10.94 1.66e+00 3.63e-01 4.34e+01 angle pdb=" N TYR A 213 " pdb=" CA TYR A 213 " pdb=" C TYR A 213 " ideal model delta sigma weight residual 110.80 123.06 -12.26 2.13e+00 2.20e-01 3.31e+01 angle pdb=" C PRO A 272 " pdb=" N LYS A 273 " pdb=" CA LYS A 273 " ideal model delta sigma weight residual 120.09 127.23 -7.14 1.25e+00 6.40e-01 3.26e+01 angle pdb=" N ILE A 330 " pdb=" CA ILE A 330 " pdb=" C ILE A 330 " ideal model delta sigma weight residual 107.99 100.27 7.72 1.46e+00 4.69e-01 2.79e+01 angle pdb=" C GLN C 22 " pdb=" N LEU C 23 " pdb=" CA LEU C 23 " ideal model delta sigma weight residual 122.82 130.01 -7.19 1.42e+00 4.96e-01 2.56e+01 ... (remaining 18356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 7756 17.38 - 34.77: 266 34.77 - 52.15: 39 52.15 - 69.53: 7 69.53 - 86.91: 5 Dihedral angle restraints: 8073 sinusoidal: 3267 harmonic: 4806 Sorted by residual: dihedral pdb=" CA ASN B 100 " pdb=" C ASN B 100 " pdb=" N ASN B 101 " pdb=" CA ASN B 101 " ideal model delta harmonic sigma weight residual -180.00 -153.55 -26.45 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C TYR A 213 " pdb=" N TYR A 213 " pdb=" CA TYR A 213 " pdb=" CB TYR A 213 " ideal model delta harmonic sigma weight residual -122.60 -135.31 12.71 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual 122.80 135.17 -12.37 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 8070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1863 0.100 - 0.200: 169 0.200 - 0.301: 2 0.301 - 0.401: 4 0.401 - 0.501: 2 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA TYR A 213 " pdb=" N TYR A 213 " pdb=" C TYR A 213 " pdb=" CB TYR A 213 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 2037 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 212 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C TYR A 212 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR A 212 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 213 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1312 " -0.026 2.00e-02 2.50e+03 1.75e-02 7.67e+00 pdb=" CG TRP A1312 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A1312 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A1312 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1312 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1312 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1312 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1312 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1312 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1312 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 245 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LEU A 245 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 245 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 246 " 0.015 2.00e-02 2.50e+03 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 50 2.48 - 3.08: 7917 3.08 - 3.69: 19347 3.69 - 4.29: 29351 4.29 - 4.90: 50060 Nonbonded interactions: 106725 Sorted by model distance: nonbonded pdb=" O GLN A1392 " pdb=" O ASN A1393 " model vdw 1.874 3.040 nonbonded pdb=" O GLN A1392 " pdb=" NE2 GLN A1392 " model vdw 2.086 2.520 nonbonded pdb=" O ARG B 126 " pdb=" CD2 LEU B 134 " model vdw 2.198 3.460 nonbonded pdb=" OG SER A 17 " pdb=" OG SER A 373 " model vdw 2.275 2.440 nonbonded pdb=" OE1 GLN A1188 " pdb=" OH TYR B 59 " model vdw 2.292 2.440 ... (remaining 106720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 10.640 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 38.610 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.005 0.052 13536 Z= 0.345 Angle : 0.916 12.262 18361 Z= 0.507 Chirality : 0.058 0.501 2040 Planarity : 0.007 0.060 2350 Dihedral : 9.746 86.913 4967 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.90 % Favored : 91.91 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.13 % 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: -3.82 (0.17), residues: 1632 helix: -4.40 (0.26), residues: 104 sheet: -1.98 (0.18), residues: 611 loop : -2.75 (0.17), residues: 917 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 400 time to evaluate : 1.650 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 406 average time/residue: 1.3113 time to fit residues: 579.2634 Evaluate side-chains 214 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.0702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 29 ASN A 246 ASN A 516 GLN A 680 HIS A 885 GLN A1095 GLN A1099 HIS A1158 ASN A1168 GLN A1177 HIS A1332 ASN A1405 ASN B 189 GLN B 191 ASN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN B 310 HIS B 325 GLN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 13536 Z= 0.248 Angle : 0.675 12.684 18361 Z= 0.339 Chirality : 0.047 0.183 2040 Planarity : 0.005 0.045 2350 Dihedral : 5.624 23.470 1796 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer Outliers : 4.91 % 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: -2.93 (0.18), residues: 1632 helix: -3.00 (0.41), residues: 104 sheet: -1.22 (0.19), residues: 616 loop : -2.39 (0.17), residues: 912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 214 time to evaluate : 1.801 Fit side-chains outliers start: 71 outliers final: 22 residues processed: 259 average time/residue: 1.2211 time to fit residues: 347.6784 Evaluate side-chains 200 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 7 average time/residue: 0.4602 time to fit residues: 6.3280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 0.0040 chunk 41 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 685 HIS A 858 GLN A 866 HIS A1089 ASN A1095 GLN A1334 HIS A1442 HIS B 189 GLN B 310 HIS C 59 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 13536 Z= 0.300 Angle : 0.685 13.940 18361 Z= 0.340 Chirality : 0.048 0.198 2040 Planarity : 0.005 0.043 2350 Dihedral : 5.522 23.660 1796 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.03 % Rotamer Outliers : 4.84 % 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: -2.39 (0.19), residues: 1632 helix: -2.53 (0.45), residues: 104 sheet: -0.79 (0.20), residues: 625 loop : -2.11 (0.19), residues: 903 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 183 time to evaluate : 1.602 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 37 residues processed: 233 average time/residue: 1.2989 time to fit residues: 331.8110 Evaluate side-chains 208 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 25 residues processed: 12 average time/residue: 0.5478 time to fit residues: 10.0703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 0.2980 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN A 866 HIS A1095 GLN A1158 ASN A1442 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 268 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 13536 Z= 0.270 Angle : 0.651 13.586 18361 Z= 0.323 Chirality : 0.046 0.184 2040 Planarity : 0.004 0.045 2350 Dihedral : 5.342 23.413 1796 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.84 % Favored : 92.10 % Rotamer Outliers : 4.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.10 (0.20), residues: 1632 helix: -2.33 (0.45), residues: 105 sheet: -0.55 (0.20), residues: 623 loop : -1.93 (0.19), residues: 904 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 169 time to evaluate : 1.904 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 39 residues processed: 217 average time/residue: 1.2988 time to fit residues: 309.5642 Evaluate side-chains 189 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 9 average time/residue: 0.4029 time to fit residues: 6.8717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS A 858 GLN A1385 HIS A1442 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13536 Z= 0.237 Angle : 0.628 13.222 18361 Z= 0.309 Chirality : 0.046 0.177 2040 Planarity : 0.004 0.049 2350 Dihedral : 5.208 23.134 1796 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.90 % Favored : 92.03 % Rotamer Outliers : 4.98 % 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: -1.90 (0.20), residues: 1632 helix: -2.04 (0.47), residues: 105 sheet: -0.43 (0.20), residues: 630 loop : -1.81 (0.20), residues: 897 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 158 time to evaluate : 1.535 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 41 residues processed: 211 average time/residue: 1.2291 time to fit residues: 285.2429 Evaluate side-chains 190 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 149 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 31 residues processed: 11 average time/residue: 0.5345 time to fit residues: 9.2566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN A 866 HIS ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1442 HIS B 189 GLN B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13536 Z= 0.248 Angle : 0.629 13.071 18361 Z= 0.311 Chirality : 0.046 0.172 2040 Planarity : 0.004 0.048 2350 Dihedral : 5.175 22.994 1796 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.16 % Rotamer Outliers : 4.08 % 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: -1.79 (0.20), residues: 1632 helix: -1.91 (0.47), residues: 105 sheet: -0.36 (0.20), residues: 636 loop : -1.75 (0.20), residues: 891 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 152 time to evaluate : 1.864 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 39 residues processed: 198 average time/residue: 1.2495 time to fit residues: 272.1454 Evaluate side-chains 188 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.590 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 7 average time/residue: 0.3016 time to fit residues: 4.8387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1442 HIS B 181 HIS B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 13536 Z= 0.271 Angle : 0.641 13.151 18361 Z= 0.316 Chirality : 0.047 0.167 2040 Planarity : 0.004 0.049 2350 Dihedral : 5.223 23.103 1796 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.69 (0.20), residues: 1632 helix: -1.81 (0.47), residues: 105 sheet: -0.28 (0.20), residues: 642 loop : -1.70 (0.20), residues: 885 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 151 time to evaluate : 1.479 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 46 residues processed: 196 average time/residue: 1.3191 time to fit residues: 284.8898 Evaluate side-chains 189 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 143 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 32 residues processed: 14 average time/residue: 0.6962 time to fit residues: 13.8992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 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 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A1237 GLN A1442 HIS B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13536 Z= 0.230 Angle : 0.617 12.922 18361 Z= 0.305 Chirality : 0.046 0.169 2040 Planarity : 0.004 0.047 2350 Dihedral : 5.109 22.681 1796 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer Outliers : 3.73 % 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: -1.61 (0.20), residues: 1632 helix: -1.60 (0.49), residues: 105 sheet: -0.24 (0.20), residues: 646 loop : -1.66 (0.20), residues: 881 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 147 time to evaluate : 1.488 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 38 residues processed: 189 average time/residue: 1.2742 time to fit residues: 264.6967 Evaluate side-chains 183 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 31 residues processed: 7 average time/residue: 0.4633 time to fit residues: 6.1000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 HIS B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13536 Z= 0.246 Angle : 0.626 12.914 18361 Z= 0.309 Chirality : 0.046 0.168 2040 Planarity : 0.004 0.048 2350 Dihedral : 5.126 22.743 1796 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer Outliers : 3.53 % 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: -1.58 (0.20), residues: 1632 helix: -1.50 (0.49), residues: 105 sheet: -0.18 (0.20), residues: 638 loop : -1.68 (0.20), residues: 889 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 1.610 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 40 residues processed: 196 average time/residue: 1.2766 time to fit residues: 275.1797 Evaluate side-chains 187 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 33 residues processed: 7 average time/residue: 0.4971 time to fit residues: 6.4796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 HIS B 69 ASN B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 13536 Z= 0.306 Angle : 0.674 12.996 18361 Z= 0.331 Chirality : 0.047 0.203 2040 Planarity : 0.004 0.051 2350 Dihedral : 5.297 23.560 1796 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer Outliers : 3.04 % 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: -1.60 (0.20), residues: 1632 helix: -1.57 (0.49), residues: 105 sheet: -0.17 (0.20), residues: 631 loop : -1.70 (0.20), residues: 896 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 1.594 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 38 residues processed: 182 average time/residue: 1.3637 time to fit residues: 272.1154 Evaluate side-chains 184 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 34 residues processed: 5 average time/residue: 0.7294 time to fit residues: 6.3855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 HIS B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.098465 restraints weight = 15681.021| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.88 r_work: 0.2995 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 13536 Z= 0.225 Angle : 0.627 12.889 18361 Z= 0.308 Chirality : 0.046 0.193 2040 Planarity : 0.004 0.049 2350 Dihedral : 5.120 23.253 1796 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.41 % Favored : 92.52 % Rotamer Outliers : 3.11 % 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: -1.51 (0.20), residues: 1632 helix: -1.38 (0.49), residues: 105 sheet: -0.12 (0.20), residues: 638 loop : -1.65 (0.20), residues: 889 =============================================================================== Job complete usr+sys time: 5405.30 seconds wall clock time: 96 minutes 18.09 seconds (5778.09 seconds total)