Starting phenix.real_space_refine on Thu Jul 31 06:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6urg_20860/07_2025/6urg_20860.cif Found real_map, /net/cci-nas-00/data/ceres_data/6urg_20860/07_2025/6urg_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/cci-nas-00/data/ceres_data/6urg_20860/07_2025/6urg_20860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6urg_20860/07_2025/6urg_20860.map" model { file = "/net/cci-nas-00/data/ceres_data/6urg_20860/07_2025/6urg_20860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6urg_20860/07_2025/6urg_20860.cif" } 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. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 10.16, per 1000 atoms: 0.77 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.6 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: 2.44 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: 5.79 Time building geometry restraints manager: 3.64 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: 0.00 - 2.45: 17880 2.45 - 4.90: 404 4.90 - 7.36: 61 7.36 - 9.81: 12 9.81 - 12.26: 4 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 3.120 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 3.040 nonbonded pdb=" OE1 GLN A1188 " pdb=" OH TYR B 59 " model vdw 2.292 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 49.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 40.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.860 ------------------------------------------------------------------------------- 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 : 0.008 0.474 13539 Z= 0.300 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 Details of bonding type rmsd hydrogen bonds : bond 0.26091 ( 340) hydrogen bonds : angle 9.73317 ( 906) metal coordination : bond 0.37802 ( 3) covalent geometry : bond 0.00520 (13536) covalent geometry : angle 0.91649 (18361) *********************** 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 to be fit. rotamer outliers: 10 poor density : 400 time to evaluate : 1.597 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: 1.3477 time to fit residues: 596.0129 Evaluate side-chains 215 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 685 HIS A 885 GLN A1095 GLN A1099 HIS A1177 HIS A1332 ASN A1405 ASN B 191 ASN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS B 325 GLN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107703 restraints weight = 15318.481| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.03 r_work: 0.3012 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13539 Z= 0.183 Angle : 0.709 13.161 18361 Z= 0.358 Chirality : 0.048 0.199 2040 Planarity : 0.005 0.046 2350 Dihedral : 6.293 84.155 1801 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 4.22 % Allowed : 13.49 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.96 (0.18), residues: 1632 helix: -3.13 (0.39), residues: 110 sheet: -1.32 (0.19), residues: 622 loop : -2.32 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1312 HIS 0.011 0.001 HIS B 374 PHE 0.027 0.002 PHE A 16 TYR 0.018 0.002 TYR A1256 ARG 0.006 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 340) hydrogen bonds : angle 6.30928 ( 906) metal coordination : bond 0.01028 ( 3) covalent geometry : bond 0.00427 (13536) covalent geometry : angle 0.70891 (18361) *********************** 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 282 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 time to evaluate : 1.538 Fit side-chains REVERT: A 199 LYS cc_start: 0.6972 (mtpt) cc_final: 0.6703 (tptm) REVERT: A 222 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 319 ARG cc_start: 0.8422 (ttt180) cc_final: 0.8105 (ttt180) REVERT: A 498 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 587 GLN cc_start: 0.8464 (tp40) cc_final: 0.8195 (mt0) REVERT: A 633 ASN cc_start: 0.8470 (m-40) cc_final: 0.8115 (m-40) REVERT: A 856 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.7920 (p) REVERT: A 982 ASN cc_start: 0.8079 (p0) cc_final: 0.7235 (m-40) REVERT: A 1146 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: B 78 ASP cc_start: 0.8114 (t0) cc_final: 0.7718 (m-30) REVERT: B 235 HIS cc_start: 0.8425 (t70) cc_final: 0.8175 (t70) REVERT: B 321 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7558 (mmmt) REVERT: B 332 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7863 (mptp) outliers start: 61 outliers final: 21 residues processed: 259 average time/residue: 1.2211 time to fit residues: 347.1718 Evaluate side-chains 199 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 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 856 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 1050 MET Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1210 LEU 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 F residue 486 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 858 GLN A 866 HIS A1332 ASN A1334 HIS A1385 HIS A1442 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 268 GLN B 310 HIS B 343 HIS ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.124463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.097155 restraints weight = 15464.456| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.09 r_work: 0.2921 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 13539 Z= 0.328 Angle : 0.831 14.542 18361 Z= 0.415 Chirality : 0.052 0.209 2040 Planarity : 0.006 0.058 2350 Dihedral : 6.138 30.891 1798 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.25 % Favored : 90.69 % Rotamer: Outliers : 5.39 % Allowed : 15.42 % Favored : 79.18 % 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: -2.54 (0.19), residues: 1632 helix: -2.63 (0.44), residues: 105 sheet: -1.01 (0.19), residues: 642 loop : -2.11 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1312 HIS 0.017 0.002 HIS B 374 PHE 0.031 0.003 PHE A 16 TYR 0.036 0.003 TYR B 187 ARG 0.009 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 340) hydrogen bonds : angle 6.09947 ( 906) metal coordination : bond 0.01150 ( 3) covalent geometry : bond 0.00800 (13536) covalent geometry : angle 0.83136 (18361) *********************** 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 255 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 177 time to evaluate : 1.426 Fit side-chains REVERT: A 129 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8001 (mtt-85) REVERT: A 237 THR cc_start: 0.8428 (p) cc_final: 0.8043 (p) REVERT: A 498 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8136 (pp) REVERT: A 587 GLN cc_start: 0.8625 (tp40) cc_final: 0.8407 (mt0) REVERT: A 872 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 982 ASN cc_start: 0.8232 (p0) cc_final: 0.7653 (m-40) REVERT: A 1063 ASP cc_start: 0.7610 (t0) cc_final: 0.7125 (OUTLIER) REVERT: A 1064 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: A 1112 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7335 (mp0) REVERT: A 1166 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7693 (mttt) REVERT: A 1186 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8576 (mt) REVERT: A 1289 GLU cc_start: 0.7958 (pm20) cc_final: 0.7704 (tt0) REVERT: B 130 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: B 210 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8114 (t80) REVERT: B 331 LYS cc_start: 0.9221 (mttp) cc_final: 0.9015 (mmtp) outliers start: 78 outliers final: 37 residues processed: 233 average time/residue: 1.2521 time to fit residues: 319.0069 Evaluate side-chains 205 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 129 ARG 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 498 LEU Chi-restraints excluded: chain A residue 620 GLN 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 703 ASP Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 872 LEU 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 1064 GLU Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1166 LYS 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 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1429 ILE 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 112 ARG Chi-restraints excluded: chain B residue 130 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 24 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 783 HIS A 858 GLN A1332 ASN A1442 HIS B 189 GLN B 268 GLN B 405 ASN C 59 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.099240 restraints weight = 15399.938| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.11 r_work: 0.2973 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.510 13539 Z= 0.218 Angle : 0.657 13.969 18361 Z= 0.330 Chirality : 0.047 0.188 2040 Planarity : 0.005 0.051 2350 Dihedral : 5.587 28.293 1798 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 4.91 % Allowed : 16.67 % Favored : 78.42 % 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: -2.26 (0.20), residues: 1632 helix: -2.32 (0.46), residues: 105 sheet: -0.77 (0.20), residues: 640 loop : -1.98 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1337 HIS 0.011 0.001 HIS B 374 PHE 0.015 0.002 PHE A 16 TYR 0.017 0.002 TYR B 187 ARG 0.004 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 340) hydrogen bonds : angle 5.71930 ( 906) metal coordination : bond 0.29441 ( 3) covalent geometry : bond 0.00383 (13536) covalent geometry : angle 0.65720 (18361) *********************** 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 243 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 1.616 Fit side-chains REVERT: A 124 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: A 237 THR cc_start: 0.8316 (p) cc_final: 0.7875 (p) REVERT: A 498 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8104 (pp) REVERT: A 516 GLN cc_start: 0.9007 (tt0) cc_final: 0.8607 (mt0) REVERT: A 633 ASN cc_start: 0.8466 (m-40) cc_final: 0.8179 (m-40) REVERT: A 686 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8433 (tptt) REVERT: A 872 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (pp) REVERT: A 982 ASN cc_start: 0.8184 (p0) cc_final: 0.7625 (m-40) REVERT: A 1063 ASP cc_start: 0.7601 (t0) cc_final: 0.7238 (t0) REVERT: A 1064 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: A 1112 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7258 (mp0) REVERT: A 1186 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8504 (mt) REVERT: A 1289 GLU cc_start: 0.7867 (pm20) cc_final: 0.7665 (tt0) REVERT: A 1294 MET cc_start: 0.8193 (ttm) cc_final: 0.7930 (mtp) REVERT: B 130 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: B 207 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: B 210 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7933 (t80) REVERT: B 279 GLN cc_start: 0.8370 (pt0) cc_final: 0.8122 (pt0) REVERT: B 321 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7745 (mmmt) REVERT: B 332 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7897 (mptp) outliers start: 71 outliers final: 30 residues processed: 223 average time/residue: 1.2877 time to fit residues: 314.1618 Evaluate side-chains 195 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 124 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 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 607 VAL 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 790 GLU Chi-restraints excluded: chain A residue 872 LEU 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 1064 GLU Chi-restraints excluded: chain A residue 1163 LEU 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 1273 ASP 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 104 ASN Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 210 PHE 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 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 118 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 783 HIS ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1332 ASN A1442 HIS B 69 ASN B 189 GLN B 268 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099701 restraints weight = 15493.428| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.09 r_work: 0.2952 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13539 Z= 0.185 Angle : 0.671 13.793 18361 Z= 0.336 Chirality : 0.048 0.184 2040 Planarity : 0.005 0.054 2350 Dihedral : 5.519 28.208 1798 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.33 % Favored : 91.61 % Rotamer: Outliers : 4.77 % Allowed : 17.50 % 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: -2.09 (0.20), residues: 1632 helix: -2.11 (0.47), residues: 105 sheet: -0.64 (0.20), residues: 640 loop : -1.89 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1337 HIS 0.011 0.001 HIS B 374 PHE 0.017 0.002 PHE A 16 TYR 0.020 0.002 TYR B 187 ARG 0.004 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 340) hydrogen bonds : angle 5.60608 ( 906) metal coordination : bond 0.00755 ( 3) covalent geometry : bond 0.00445 (13536) covalent geometry : angle 0.67142 (18361) *********************** 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 229 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 160 time to evaluate : 1.629 Fit side-chains REVERT: A 124 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: A 237 THR cc_start: 0.8449 (p) cc_final: 0.7993 (p) REVERT: A 378 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7341 (mt-10) REVERT: A 498 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8111 (pp) REVERT: A 594 GLU cc_start: 0.8288 (tt0) cc_final: 0.8006 (tt0) REVERT: A 633 ASN cc_start: 0.8452 (m-40) cc_final: 0.8138 (m-40) REVERT: A 872 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8088 (pp) REVERT: A 982 ASN cc_start: 0.8146 (p0) cc_final: 0.7579 (m-40) REVERT: A 1063 ASP cc_start: 0.7652 (t0) cc_final: 0.7384 (t0) REVERT: A 1064 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: A 1112 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7337 (mp0) REVERT: A 1186 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 1289 GLU cc_start: 0.7909 (pm20) cc_final: 0.7704 (tt0) REVERT: A 1294 MET cc_start: 0.8268 (ttm) cc_final: 0.8026 (mtp) REVERT: B 130 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: B 207 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: B 210 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7983 (t80) REVERT: B 321 LYS cc_start: 0.8013 (mmpt) cc_final: 0.7782 (mmmt) REVERT: B 332 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7867 (mptp) outliers start: 69 outliers final: 39 residues processed: 210 average time/residue: 1.3316 time to fit residues: 306.3490 Evaluate side-chains 203 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 124 GLU 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 257 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN 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 790 GLU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 872 LEU 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 1064 GLU Chi-restraints excluded: chain A residue 1163 LEU 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 1332 ASN 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 104 ASN Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 210 PHE 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 346 LEU Chi-restraints excluded: chain B residue 367 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 110 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN A 587 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1442 HIS B 160 HIS B 189 GLN B 268 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098289 restraints weight = 15523.430| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.13 r_work: 0.2906 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13539 Z= 0.166 Angle : 0.655 13.646 18361 Z= 0.328 Chirality : 0.047 0.240 2040 Planarity : 0.004 0.053 2350 Dihedral : 5.391 27.881 1798 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.54 % Favored : 92.40 % Rotamer: Outliers : 4.50 % Allowed : 18.12 % 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: -1.96 (0.20), residues: 1632 helix: -1.91 (0.48), residues: 105 sheet: -0.54 (0.20), residues: 645 loop : -1.83 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1337 HIS 0.009 0.001 HIS B 374 PHE 0.016 0.002 PHE A 16 TYR 0.017 0.001 TYR B 187 ARG 0.004 0.000 ARG A1109 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 340) hydrogen bonds : angle 5.53926 ( 906) metal coordination : bond 0.00560 ( 3) covalent geometry : bond 0.00399 (13536) covalent geometry : angle 0.65454 (18361) *********************** 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 227 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 1.532 Fit side-chains REVERT: A 124 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: A 199 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7083 (tmtt) REVERT: A 237 THR cc_start: 0.8475 (p) cc_final: 0.8045 (p) REVERT: A 378 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7325 (mt-10) REVERT: A 498 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8221 (pp) REVERT: A 580 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6817 (tt0) REVERT: A 594 GLU cc_start: 0.8336 (tt0) cc_final: 0.8026 (tt0) REVERT: A 633 ASN cc_start: 0.8498 (m-40) cc_final: 0.8198 (m-40) REVERT: A 872 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 982 ASN cc_start: 0.8149 (p0) cc_final: 0.7545 (m-40) REVERT: A 996 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8790 (tm) REVERT: A 1063 ASP cc_start: 0.7675 (t0) cc_final: 0.7380 (t0) REVERT: A 1064 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: A 1112 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7242 (mp0) REVERT: A 1186 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 1289 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: A 1294 MET cc_start: 0.8148 (ttm) cc_final: 0.7910 (mtp) REVERT: B 130 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (pm20) REVERT: B 207 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: B 210 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7955 (t80) REVERT: B 321 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7760 (mmmt) REVERT: B 332 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7889 (mptp) outliers start: 65 outliers final: 38 residues processed: 206 average time/residue: 1.2980 time to fit residues: 292.9969 Evaluate side-chains 198 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER 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 124 GLU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 590 GLN 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 790 GLU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 872 LEU 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 1064 GLU Chi-restraints excluded: chain A residue 1162 VAL 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 1289 GLU 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 104 ASN Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 210 PHE 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 367 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 34 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 chunk 153 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 ASN A1442 HIS B 189 GLN B 268 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.100483 restraints weight = 15502.047| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.09 r_work: 0.2921 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13539 Z= 0.147 Angle : 0.640 13.499 18361 Z= 0.318 Chirality : 0.047 0.217 2040 Planarity : 0.004 0.053 2350 Dihedral : 5.237 27.536 1798 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 4.84 % Allowed : 18.53 % Favored : 76.63 % 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: -1.83 (0.20), residues: 1632 helix: -1.75 (0.49), residues: 105 sheet: -0.44 (0.20), residues: 647 loop : -1.77 (0.20), residues: 880 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 0.015 0.001 TYR B 187 ARG 0.003 0.000 ARG A1109 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 340) hydrogen bonds : angle 5.41062 ( 906) metal coordination : bond 0.00482 ( 3) covalent geometry : bond 0.00349 (13536) covalent geometry : angle 0.63973 (18361) *********************** 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 228 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 158 time to evaluate : 1.556 Fit side-chains REVERT: A 124 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8324 (pt0) REVERT: A 199 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7079 (tmtt) REVERT: A 237 THR cc_start: 0.8471 (p) cc_final: 0.8046 (p) REVERT: A 378 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7357 (mt-10) REVERT: A 498 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8255 (pp) REVERT: A 580 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6830 (tt0) REVERT: A 593 MET cc_start: 0.7785 (mmm) cc_final: 0.7514 (mmm) REVERT: A 594 GLU cc_start: 0.8369 (tt0) cc_final: 0.8086 (tt0) REVERT: A 633 ASN cc_start: 0.8456 (m-40) cc_final: 0.8152 (m-40) REVERT: A 703 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 982 ASN cc_start: 0.8111 (p0) cc_final: 0.7472 (m-40) REVERT: A 1063 ASP cc_start: 0.7653 (t0) cc_final: 0.7358 (t0) REVERT: A 1064 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: A 1112 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7207 (mp0) REVERT: A 1186 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8521 (mt) REVERT: A 1294 MET cc_start: 0.8084 (ttm) cc_final: 0.7830 (mtp) REVERT: A 1383 MET cc_start: 0.8562 (mtp) cc_final: 0.8210 (mtt) REVERT: B 130 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: B 207 GLU cc_start: 0.8460 (tp30) cc_final: 0.7649 (tt0) REVERT: B 210 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7965 (t80) REVERT: B 321 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7726 (mmmt) REVERT: B 332 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7869 (mptp) outliers start: 70 outliers final: 42 residues processed: 209 average time/residue: 1.3523 time to fit residues: 308.5375 Evaluate side-chains 201 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 124 GLU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 590 GLN 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 649 CYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 703 ASP Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS 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 1064 GLU Chi-restraints excluded: chain A residue 1163 LEU 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 1332 ASN 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 104 ASN Chi-restraints excluded: chain B residue 130 GLU 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 332 LYS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 VAL 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 17 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 63 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 ASN A1442 HIS B 189 GLN B 268 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.099436 restraints weight = 15461.683| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.10 r_work: 0.2922 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13539 Z= 0.156 Angle : 0.648 13.452 18361 Z= 0.322 Chirality : 0.047 0.216 2040 Planarity : 0.004 0.051 2350 Dihedral : 5.241 27.628 1798 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.41 % Favored : 92.52 % Rotamer: Outliers : 4.63 % Allowed : 18.95 % 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: -1.77 (0.20), residues: 1632 helix: -1.60 (0.50), residues: 105 sheet: -0.41 (0.20), residues: 647 loop : -1.73 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1337 HIS 0.009 0.001 HIS B 374 PHE 0.015 0.001 PHE A 16 TYR 0.015 0.001 TYR B 187 ARG 0.003 0.000 ARG A1109 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 340) hydrogen bonds : angle 5.38675 ( 906) metal coordination : bond 0.00471 ( 3) covalent geometry : bond 0.00373 (13536) covalent geometry : angle 0.64781 (18361) *********************** 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 225 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 1.814 Fit side-chains REVERT: A 124 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8317 (pt0) REVERT: A 199 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7192 (tmtt) REVERT: A 237 THR cc_start: 0.8473 (p) cc_final: 0.8047 (p) REVERT: A 378 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7359 (mt-10) REVERT: A 580 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6808 (tt0) REVERT: A 593 MET cc_start: 0.7795 (mmm) cc_final: 0.7523 (mmm) REVERT: A 594 GLU cc_start: 0.8389 (tt0) cc_final: 0.8100 (tt0) REVERT: A 633 ASN cc_start: 0.8423 (m-40) cc_final: 0.8121 (m-40) REVERT: A 982 ASN cc_start: 0.8109 (p0) cc_final: 0.7470 (m-40) REVERT: A 1063 ASP cc_start: 0.7691 (t0) cc_final: 0.7489 (t0) REVERT: A 1112 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7224 (mp0) REVERT: A 1186 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8525 (mt) REVERT: A 1294 MET cc_start: 0.8080 (ttm) cc_final: 0.7826 (mtp) REVERT: A 1383 MET cc_start: 0.8581 (mtp) cc_final: 0.8234 (mtt) REVERT: B 130 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: B 207 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: B 210 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8003 (t80) REVERT: B 321 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7704 (mmmt) REVERT: B 332 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7857 (mptp) outliers start: 67 outliers final: 44 residues processed: 202 average time/residue: 1.5271 time to fit residues: 337.7355 Evaluate side-chains 203 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 152 time to evaluate : 1.892 ------------------------------------------------------------------------------- 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 124 GLU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 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 782 THR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS 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 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 1332 ASN 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 104 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 239 ILE 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 346 LEU Chi-restraints excluded: chain B residue 367 VAL 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 97 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 11 optimal weight: 0.0670 chunk 55 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 A1332 ASN A1442 HIS B 268 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101972 restraints weight = 15361.125| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.96 r_work: 0.2989 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13539 Z= 0.148 Angle : 0.638 13.395 18361 Z= 0.316 Chirality : 0.047 0.211 2040 Planarity : 0.004 0.048 2350 Dihedral : 5.198 27.533 1798 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.41 % Favored : 92.52 % Rotamer: Outliers : 3.87 % Allowed : 19.99 % Favored : 76.14 % 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: -1.72 (0.20), residues: 1632 helix: -1.69 (0.49), residues: 111 sheet: -0.37 (0.20), residues: 641 loop : -1.67 (0.20), residues: 880 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 B 217 TYR 0.014 0.001 TYR B 187 ARG 0.003 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 340) hydrogen bonds : angle 5.33862 ( 906) metal coordination : bond 0.00450 ( 3) covalent geometry : bond 0.00353 (13536) covalent geometry : angle 0.63758 (18361) *********************** 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 210 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 1.569 Fit side-chains REVERT: A 124 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8282 (pt0) REVERT: A 199 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7232 (tmtt) REVERT: A 237 THR cc_start: 0.8430 (p) cc_final: 0.8006 (p) REVERT: A 378 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7340 (mt-10) REVERT: A 580 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6808 (tt0) REVERT: A 593 MET cc_start: 0.7731 (mmm) cc_final: 0.7479 (mmm) REVERT: A 633 ASN cc_start: 0.8402 (m-40) cc_final: 0.8121 (m-40) REVERT: A 982 ASN cc_start: 0.8088 (p0) cc_final: 0.7446 (m-40) REVERT: A 1063 ASP cc_start: 0.7642 (t0) cc_final: 0.7395 (t0) REVERT: A 1064 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 1112 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7236 (mp0) REVERT: A 1186 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 1294 MET cc_start: 0.7981 (ttm) cc_final: 0.7712 (mtp) REVERT: A 1383 MET cc_start: 0.8512 (mtp) cc_final: 0.8155 (mtt) REVERT: B 130 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: B 207 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: B 210 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 321 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7684 (mmmt) REVERT: B 332 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7827 (mptp) outliers start: 56 outliers final: 42 residues processed: 195 average time/residue: 1.4871 time to fit residues: 319.1464 Evaluate side-chains 200 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 2.258 ------------------------------------------------------------------------------- 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 124 GLU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 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 782 THR Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS 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 1064 GLU 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 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 104 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 239 ILE 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 346 LEU Chi-restraints excluded: chain B residue 367 VAL 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 65 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 A1332 ASN A1442 HIS B 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.124733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.097898 restraints weight = 15518.084| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.09 r_work: 0.2962 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13539 Z= 0.165 Angle : 0.653 13.426 18361 Z= 0.324 Chirality : 0.047 0.220 2040 Planarity : 0.004 0.050 2350 Dihedral : 5.235 27.821 1798 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.16 % Rotamer: Outliers : 3.80 % Allowed : 20.12 % Favored : 76.07 % 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: -1.69 (0.48), residues: 111 sheet: -0.33 (0.20), residues: 646 loop : -1.67 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1337 HIS 0.006 0.001 HIS B 384 PHE 0.015 0.002 PHE A 16 TYR 0.015 0.001 TYR B 187 ARG 0.003 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 340) hydrogen bonds : angle 5.36756 ( 906) metal coordination : bond 0.00511 ( 3) covalent geometry : bond 0.00396 (13536) covalent geometry : angle 0.65269 (18361) ********************** 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 208 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 1.940 Fit side-chains REVERT: A 124 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8308 (pt0) REVERT: A 199 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7204 (tmtt) REVERT: A 237 THR cc_start: 0.8448 (p) cc_final: 0.8019 (p) REVERT: A 378 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7387 (mt-10) REVERT: A 580 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6816 (tt0) REVERT: A 593 MET cc_start: 0.7759 (mmm) cc_final: 0.7493 (mmm) REVERT: A 633 ASN cc_start: 0.8414 (m-40) cc_final: 0.8134 (m-40) REVERT: A 707 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8253 (ptp) REVERT: A 982 ASN cc_start: 0.8091 (p0) cc_final: 0.7465 (m-40) REVERT: A 1063 ASP cc_start: 0.7600 (t0) cc_final: 0.7383 (t0) REVERT: A 1064 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: A 1112 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7249 (mp0) REVERT: A 1186 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 1294 MET cc_start: 0.8095 (ttm) cc_final: 0.7829 (mtp) REVERT: B 130 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: B 207 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: B 210 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8019 (t80) REVERT: B 321 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7606 (mmmt) REVERT: B 332 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7877 (mptp) outliers start: 55 outliers final: 44 residues processed: 192 average time/residue: 1.2841 time to fit residues: 270.9257 Evaluate side-chains 202 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 149 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 124 GLU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 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 707 MET Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 897 HIS 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 1064 GLU 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 1332 ASN 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 104 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 239 ILE 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 346 LEU Chi-restraints excluded: chain B residue 367 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 145 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100844 restraints weight = 15402.843| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.98 r_work: 0.2975 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13539 Z= 0.165 Angle : 0.653 13.447 18361 Z= 0.323 Chirality : 0.047 0.218 2040 Planarity : 0.004 0.053 2350 Dihedral : 5.229 27.840 1798 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.46 % Rotamer: Outliers : 3.87 % Allowed : 19.85 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.64 (0.48), residues: 111 sheet: -0.34 (0.20), residues: 641 loop : -1.65 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1337 HIS 0.007 0.001 HIS A1334 PHE 0.014 0.002 PHE A1443 TYR 0.015 0.001 TYR B 187 ARG 0.003 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 340) hydrogen bonds : angle 5.34618 ( 906) metal coordination : bond 0.00512 ( 3) covalent geometry : bond 0.00396 (13536) covalent geometry : angle 0.65297 (18361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10500.12 seconds wall clock time: 184 minutes 19.81 seconds (11059.81 seconds total)