Starting phenix.real_space_refine on Thu Feb 15 19:32:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/02_2024/6urg_20860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/02_2024/6urg_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_20860/02_2024/6urg_20860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/02_2024/6urg_20860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/02_2024/6urg_20860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6urg_20860/02_2024/6urg_20860.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.83, per 1000 atoms: 0.52 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: 5.00 Conformation dependent library (CDL) restraints added in 2.4 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: 1.85 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: 5.97 Time building geometry restraints manager: 5.47 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.110 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 40.890 Find NCS groups from input model: 0.370 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.980 ------------------------------------------------------------------------------- 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 % Allowed : 1.80 % Favored : 97.51 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A1312 HIS 0.013 0.002 HIS B 374 PHE 0.037 0.003 PHE A1074 TYR 0.035 0.003 TYR A1256 ARG 0.009 0.001 ARG A 962 *********************** 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 : 1.534 Fit side-chains revert: symmetry clash REVERT: A 1392 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: C 33 MET cc_start: 0.7340 (mtp) cc_final: 0.7020 (mtp) outliers start: 10 outliers final: 1 residues processed: 406 average time/residue: 1.2841 time to fit residues: 567.8856 Evaluate side-chains 215 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain F residue 486 LEU 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 A1392 GLN A1405 ASN 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: 0.2687 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= 0.250 Angle : 0.675 12.331 18361 Z= 0.339 Chirality : 0.047 0.183 2040 Planarity : 0.005 0.045 2350 Dihedral : 6.089 73.236 1801 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 4.91 % Allowed : 13.42 % Favored : 81.67 % 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: -3.01 (0.41), residues: 104 sheet: -1.23 (0.19), residues: 616 loop : -2.39 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1312 HIS 0.011 0.001 HIS B 374 PHE 0.026 0.002 PHE A 16 TYR 0.016 0.002 TYR A1256 ARG 0.005 0.001 ARG B 404 *********************** 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 287 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 216 time to evaluate : 1.264 Fit side-chains REVERT: A 498 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8405 (pp) REVERT: B 332 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7314 (mptp) outliers start: 71 outliers final: 23 residues processed: 260 average time/residue: 1.1615 time to fit residues: 331.7879 Evaluate side-chains 204 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 124 optimal weight: 0.6980 chunk 102 optimal weight: 0.0370 chunk 41 optimal weight: 0.2980 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 783 HIS A 858 GLN A 866 HIS A1089 ASN A1095 GLN A1332 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 HIS B 189 GLN B 310 HIS C 59 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13536 Z= 0.190 Angle : 0.619 13.374 18361 Z= 0.306 Chirality : 0.046 0.199 2040 Planarity : 0.004 0.041 2350 Dihedral : 5.215 27.036 1798 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 4.15 % Allowed : 15.77 % Favored : 80.08 % 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: -2.33 (0.19), residues: 1632 helix: -2.46 (0.45), residues: 104 sheet: -0.75 (0.20), residues: 623 loop : -2.06 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1337 HIS 0.010 0.001 HIS B 374 PHE 0.017 0.002 PHE A 16 TYR 0.013 0.001 TYR A 345 ARG 0.004 0.000 ARG B 404 *********************** 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 246 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 186 time to evaluate : 2.014 Fit side-chains revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 1146 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6436 (tp30) REVERT: A 1186 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8644 (mt) REVERT: B 78 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: F 474 ASP cc_start: 0.7857 (t0) cc_final: 0.7567 (t0) outliers start: 60 outliers final: 30 residues processed: 225 average time/residue: 1.2517 time to fit residues: 309.8639 Evaluate side-chains 202 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 1429 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 858 GLN A 866 HIS A1095 GLN A1334 HIS A1385 HIS A1442 HIS B 189 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13536 Z= 0.380 Angle : 0.718 13.738 18361 Z= 0.357 Chirality : 0.049 0.180 2040 Planarity : 0.005 0.047 2350 Dihedral : 5.631 29.160 1798 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.52 % Favored : 91.42 % Rotamer: Outliers : 5.26 % Allowed : 15.77 % Favored : 78.98 % 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: -2.18 (0.20), residues: 1632 helix: -2.40 (0.45), residues: 105 sheet: -0.63 (0.20), residues: 629 loop : -1.96 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1312 HIS 0.014 0.002 HIS B 374 PHE 0.023 0.002 PHE A 16 TYR 0.031 0.002 TYR B 187 ARG 0.006 0.001 ARG B 404 *********************** 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 245 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 169 time to evaluate : 1.596 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8360 (pp) REVERT: A 498 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8467 (pp) REVERT: A 1064 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: A 1095 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: A 1146 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6464 (tp30) REVERT: A 1166 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7618 (mttt) REVERT: A 1237 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.6248 (mp-120) REVERT: A 1294 MET cc_start: 0.7160 (ttm) cc_final: 0.6868 (mtp) REVERT: B 78 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8371 (m-30) REVERT: B 210 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7703 (t80) outliers start: 76 outliers final: 38 residues processed: 223 average time/residue: 1.3185 time to fit residues: 320.9006 Evaluate side-chains 199 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1095 GLN Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LYS Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1237 GLN Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 81 optimal weight: 0.0670 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 0.0040 overall best weight: 0.4130 ------------------------------------------------------------------------------- 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 A1332 ASN A1442 HIS B 189 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13536 Z= 0.186 Angle : 0.599 13.158 18361 Z= 0.298 Chirality : 0.045 0.185 2040 Planarity : 0.004 0.046 2350 Dihedral : 5.151 27.141 1798 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 4.01 % Allowed : 18.26 % Favored : 77.73 % 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: -1.93 (0.20), residues: 1632 helix: -2.08 (0.46), residues: 105 sheet: -0.44 (0.20), residues: 627 loop : -1.84 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1337 HIS 0.009 0.001 HIS B 374 PHE 0.014 0.001 PHE A 16 TYR 0.013 0.001 TYR B 187 ARG 0.003 0.000 ARG B 404 *********************** 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 228 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 170 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 498 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 1294 MET cc_start: 0.6754 (ttm) cc_final: 0.6420 (mtp) REVERT: B 210 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7590 (t80) outliers start: 58 outliers final: 31 residues processed: 209 average time/residue: 1.2382 time to fit residues: 283.6257 Evaluate side-chains 188 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 13 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 A1071 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: 0.7862 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13536 Z= 0.193 Angle : 0.593 12.995 18361 Z= 0.294 Chirality : 0.045 0.176 2040 Planarity : 0.004 0.046 2350 Dihedral : 5.015 26.926 1798 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 4.22 % Allowed : 18.40 % Favored : 77.39 % 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: -1.74 (0.20), residues: 1632 helix: -1.95 (0.46), residues: 111 sheet: -0.31 (0.20), residues: 632 loop : -1.71 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1337 HIS 0.009 0.001 HIS B 374 PHE 0.014 0.001 PHE A 16 TYR 0.014 0.001 TYR B 187 ARG 0.003 0.000 ARG B 404 *********************** 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 216 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8205 (pp) REVERT: A 498 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8416 (pp) REVERT: A 1294 MET cc_start: 0.6684 (ttm) cc_final: 0.6372 (mtp) REVERT: B 210 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7584 (t80) outliers start: 61 outliers final: 33 residues processed: 197 average time/residue: 1.3309 time to fit residues: 286.4614 Evaluate side-chains 192 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 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: 0.8980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** A1237 GLN A1442 HIS B 189 GLN B 243 HIS B 268 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: 0.7893 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13536 Z= 0.252 Angle : 0.622 12.953 18361 Z= 0.310 Chirality : 0.046 0.235 2040 Planarity : 0.004 0.049 2350 Dihedral : 5.136 27.520 1798 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.46 % Rotamer: Outliers : 4.15 % Allowed : 18.74 % Favored : 77.11 % 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: -1.67 (0.20), residues: 1632 helix: -1.87 (0.46), residues: 111 sheet: -0.28 (0.20), residues: 636 loop : -1.66 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1312 HIS 0.010 0.001 HIS B 374 PHE 0.017 0.002 PHE A 16 TYR 0.019 0.002 TYR B 187 ARG 0.005 0.000 ARG A1274 *********************** 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: 60 poor density : 155 time to evaluate : 1.664 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8282 (pp) REVERT: A 498 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8423 (pp) REVERT: A 996 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8418 (tm) REVERT: A 1146 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6549 (tp30) REVERT: A 1294 MET cc_start: 0.6777 (ttm) cc_final: 0.6496 (mtp) REVERT: B 210 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7706 (t80) outliers start: 60 outliers final: 37 residues processed: 194 average time/residue: 1.2426 time to fit residues: 265.9192 Evaluate side-chains 190 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.9262 ------------------------------------------------------------------------------- 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** A1237 GLN A1442 HIS B 243 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: 0.7927 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13536 Z= 0.315 Angle : 0.661 13.111 18361 Z= 0.330 Chirality : 0.048 0.221 2040 Planarity : 0.004 0.051 2350 Dihedral : 5.326 27.982 1798 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 4.08 % Allowed : 18.53 % Favored : 77.39 % 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: -1.66 (0.20), residues: 1632 helix: -1.86 (0.47), residues: 111 sheet: -0.26 (0.20), residues: 639 loop : -1.66 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1312 HIS 0.012 0.001 HIS B 374 PHE 0.019 0.002 PHE A 16 TYR 0.023 0.002 TYR B 187 ARG 0.007 0.000 ARG A1274 *********************** 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 210 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 151 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 498 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8489 (pp) REVERT: A 1146 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6608 (tp30) REVERT: A 1294 MET cc_start: 0.6878 (ttm) cc_final: 0.6580 (mtp) REVERT: B 210 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7764 (t80) outliers start: 59 outliers final: 39 residues processed: 194 average time/residue: 1.2402 time to fit residues: 263.6531 Evaluate side-chains 191 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.8980 chunk 139 optimal weight: 0.0970 chunk 148 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13536 Z= 0.234 Angle : 0.619 12.898 18361 Z= 0.309 Chirality : 0.046 0.227 2040 Planarity : 0.004 0.050 2350 Dihedral : 5.173 27.975 1798 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 3.32 % Allowed : 19.57 % Favored : 77.11 % 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: -1.61 (0.20), residues: 1632 helix: -1.72 (0.48), residues: 111 sheet: -0.20 (0.20), residues: 635 loop : -1.66 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1337 HIS 0.010 0.001 HIS B 374 PHE 0.015 0.001 PHE A 16 TYR 0.018 0.001 TYR B 187 ARG 0.006 0.000 ARG A1274 *********************** 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 201 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 153 time to evaluate : 1.562 Fit side-chains REVERT: A 388 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8352 (pp) REVERT: A 498 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8518 (pp) REVERT: A 996 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8425 (tm) REVERT: A 1146 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6569 (tp30) REVERT: A 1237 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.5646 (mp-120) REVERT: A 1294 MET cc_start: 0.6708 (ttm) cc_final: 0.6390 (mtp) REVERT: A 1383 MET cc_start: 0.7696 (mtp) cc_final: 0.7493 (mtt) REVERT: B 210 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7679 (t80) outliers start: 48 outliers final: 32 residues processed: 188 average time/residue: 1.2695 time to fit residues: 260.7703 Evaluate side-chains 187 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1237 GLN Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU 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: 1.9990 chunk 108 optimal weight: 0.7980 chunk 164 optimal weight: 0.0470 chunk 151 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 0.0040 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.4490 ------------------------------------------------------------------------------- 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** A1237 GLN A1442 HIS B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13536 Z= 0.197 Angle : 0.603 12.674 18361 Z= 0.300 Chirality : 0.046 0.223 2040 Planarity : 0.004 0.048 2350 Dihedral : 5.044 27.183 1798 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 3.04 % Allowed : 19.99 % Favored : 76.97 % 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: -1.53 (0.20), residues: 1632 helix: -1.60 (0.48), residues: 111 sheet: -0.16 (0.21), residues: 630 loop : -1.61 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1337 HIS 0.009 0.001 HIS B 374 PHE 0.013 0.001 PHE A 16 TYR 0.014 0.001 TYR A 19 ARG 0.007 0.000 ARG A1235 ********************** 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 194 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.494 Fit side-chains REVERT: A 388 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8349 (pp) REVERT: A 498 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8565 (pp) REVERT: A 996 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8396 (tm) REVERT: A 1146 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6561 (tp30) REVERT: A 1294 MET cc_start: 0.6543 (ttm) cc_final: 0.6234 (mtp) REVERT: B 210 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7637 (t80) outliers start: 44 outliers final: 29 residues processed: 182 average time/residue: 1.2438 time to fit residues: 248.3580 Evaluate side-chains 180 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 686 LYS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 516 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1442 HIS B 181 HIS B 268 GLN B 319 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099189 restraints weight = 15315.346| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.93 r_work: 0.2914 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4160 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= 0.356 Angle : 0.692 13.148 18361 Z= 0.344 Chirality : 0.048 0.218 2040 Planarity : 0.004 0.056 2350 Dihedral : 5.425 28.658 1798 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.39 % Favored : 91.54 % Rotamer: Outliers : 2.97 % Allowed : 20.61 % Favored : 76.42 % 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: -1.59 (0.20), residues: 1632 helix: -1.79 (0.47), residues: 111 sheet: -0.22 (0.20), residues: 648 loop : -1.64 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1312 HIS 0.013 0.001 HIS B 374 PHE 0.020 0.002 PHE A 16 TYR 0.026 0.002 TYR B 187 ARG 0.006 0.000 ARG A1274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5364.32 seconds wall clock time: 95 minutes 42.78 seconds (5742.78 seconds total)