Starting phenix.real_space_refine on Wed Mar 4 11:15:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6urg_20860/03_2026/6urg_20860.cif Found real_map, /net/cci-nas-00/data/ceres_data/6urg_20860/03_2026/6urg_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_20860/03_2026/6urg_20860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6urg_20860/03_2026/6urg_20860.map" model { file = "/net/cci-nas-00/data/ceres_data/6urg_20860/03_2026/6urg_20860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6urg_20860/03_2026/6urg_20860.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.96, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 609.0 milliseconds 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: 0.57 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: 2.69 Time building geometry restraints manager: 1.42 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: 3.120 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- 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 : 7.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.009 0.001 ARG A 962 TYR 0.035 0.003 TYR A1256 PHE 0.037 0.003 PHE A1074 TRP 0.046 0.003 TRP A1312 HIS 0.013 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00520 (13536) covalent geometry : angle 0.91649 (18361) hydrogen bonds : bond 0.26091 ( 340) hydrogen bonds : angle 9.73317 ( 906) metal coordination : bond 0.37802 ( 3) *********************** 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 : 0.505 Fit side-chains revert: symmetry clash REVERT: A 1392 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.7007 (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: 0.6201 time to fit residues: 273.1492 Evaluate side-chains 216 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 29 ASN A 246 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.106496 restraints weight = 15481.397| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.03 r_work: 0.3061 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13539 Z= 0.186 Angle : 0.714 13.242 18361 Z= 0.360 Chirality : 0.048 0.192 2040 Planarity : 0.005 0.047 2350 Dihedral : 6.343 85.158 1801 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.29 % Favored : 92.65 % Rotamer: Outliers : 4.56 % Allowed : 13.00 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.18), residues: 1632 helix: -3.16 (0.39), residues: 110 sheet: -1.32 (0.19), residues: 627 loop : -2.35 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 404 TYR 0.019 0.002 TYR A1256 PHE 0.028 0.002 PHE A 16 TRP 0.031 0.002 TRP A1312 HIS 0.012 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00437 (13536) covalent geometry : angle 0.71444 (18361) hydrogen bonds : bond 0.04432 ( 340) hydrogen bonds : angle 6.33735 ( 906) metal coordination : bond 0.01451 ( 3) *********************** 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 283 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 0.585 Fit side-chains REVERT: A 222 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 319 ARG cc_start: 0.8435 (ttt180) cc_final: 0.8121 (ttt180) REVERT: A 498 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8051 (pp) REVERT: A 587 GLN cc_start: 0.8472 (tp40) cc_final: 0.8180 (mt0) REVERT: A 633 ASN cc_start: 0.8491 (m-40) cc_final: 0.8127 (m-40) REVERT: A 856 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.7915 (p) REVERT: A 982 ASN cc_start: 0.8092 (p0) cc_final: 0.7275 (m-40) REVERT: A 1146 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: A 1186 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 1289 GLU cc_start: 0.7671 (pm20) cc_final: 0.7471 (pm20) REVERT: B 235 HIS cc_start: 0.8434 (t70) cc_final: 0.8207 (t70) REVERT: B 321 LYS cc_start: 0.7795 (mmmt) cc_final: 0.7536 (mmmt) REVERT: B 332 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7847 (mptp) outliers start: 66 outliers final: 24 residues processed: 258 average time/residue: 0.5858 time to fit residues: 165.1802 Evaluate side-chains 201 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 162 LEU 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 1163 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1186 ILE 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 135 VAL 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 96 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 28 optimal weight: 0.0670 chunk 143 optimal weight: 0.0070 chunk 162 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS A 858 GLN A 866 HIS A1332 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 HIS B 83 GLN B 189 GLN B 310 HIS C 59 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109843 restraints weight = 15582.013| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.04 r_work: 0.3054 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.443 13539 Z= 0.166 Angle : 0.607 13.734 18361 Z= 0.305 Chirality : 0.046 0.203 2040 Planarity : 0.004 0.045 2350 Dihedral : 5.152 25.043 1798 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.50 % Favored : 93.44 % Rotamer: Outliers : 3.60 % Allowed : 15.98 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.19), residues: 1632 helix: -2.52 (0.44), residues: 109 sheet: -0.83 (0.20), residues: 623 loop : -2.07 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 616 TYR 0.010 0.001 TYR A1256 PHE 0.013 0.001 PHE A 16 TRP 0.016 0.001 TRP A1337 HIS 0.008 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00242 (13536) covalent geometry : angle 0.60737 (18361) hydrogen bonds : bond 0.03526 ( 340) hydrogen bonds : angle 5.72776 ( 906) metal coordination : bond 0.25562 ( 3) *********************** 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 254 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.519 Fit side-chains REVERT: A 222 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 319 ARG cc_start: 0.8327 (ttt180) cc_final: 0.8102 (ttt180) REVERT: A 498 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8063 (pp) REVERT: A 633 ASN cc_start: 0.8301 (m-40) cc_final: 0.8014 (m-40) REVERT: A 667 MET cc_start: 0.8372 (ttp) cc_final: 0.8148 (ttm) REVERT: A 707 MET cc_start: 0.8634 (ptp) cc_final: 0.8034 (ptp) REVERT: A 1063 ASP cc_start: 0.7438 (t0) cc_final: 0.7091 (t70) REVERT: A 1146 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: A 1289 GLU cc_start: 0.7401 (pm20) cc_final: 0.7105 (tt0) REVERT: A 1420 LYS cc_start: 0.7622 (mmtm) cc_final: 0.7270 (mmtt) REVERT: B 130 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: B 207 GLU cc_start: 0.8344 (tp30) cc_final: 0.7770 (tt0) REVERT: B 279 GLN cc_start: 0.8420 (pt0) cc_final: 0.8072 (pt0) REVERT: B 321 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7459 (mmmt) REVERT: C 33 MET cc_start: 0.7397 (mtp) cc_final: 0.7187 (mtp) REVERT: F 474 ASP cc_start: 0.8650 (t0) cc_final: 0.8431 (t0) outliers start: 52 outliers final: 20 residues processed: 237 average time/residue: 0.5877 time to fit residues: 153.1039 Evaluate side-chains 193 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1332 ASN Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 247 VAL 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 93 optimal weight: 2.9990 chunk 142 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 137 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A 858 GLN A 866 HIS A1332 ASN A1334 HIS ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1385 HIS A1442 HIS B 83 GLN B 189 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.130280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103746 restraints weight = 15523.091| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.03 r_work: 0.3016 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3379 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 : 0.665 13.730 18361 Z= 0.333 Chirality : 0.047 0.181 2040 Planarity : 0.005 0.052 2350 Dihedral : 5.363 27.730 1798 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.46 % Rotamer: Outliers : 4.98 % Allowed : 16.25 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.20), residues: 1632 helix: -2.31 (0.45), residues: 104 sheet: -0.62 (0.20), residues: 623 loop : -1.95 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 404 TYR 0.020 0.002 TYR B 187 PHE 0.020 0.002 PHE A 16 TRP 0.019 0.002 TRP A1312 HIS 0.011 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00442 (13536) covalent geometry : angle 0.66506 (18361) hydrogen bonds : bond 0.03630 ( 340) hydrogen bonds : angle 5.55968 ( 906) metal coordination : bond 0.01150 ( 3) *********************** 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 238 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 166 time to evaluate : 0.527 Fit side-chains REVERT: A 319 ARG cc_start: 0.8420 (ttt180) cc_final: 0.8189 (ttt180) REVERT: A 498 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8071 (pp) REVERT: A 633 ASN cc_start: 0.8351 (m-40) cc_final: 0.8041 (m-40) REVERT: A 1063 ASP cc_start: 0.7532 (t0) cc_final: 0.7243 (t0) REVERT: A 1112 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7166 (mp0) REVERT: A 1146 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: A 1186 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8479 (mt) REVERT: A 1289 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: A 1294 MET cc_start: 0.8036 (ttm) cc_final: 0.7757 (mtp) REVERT: A 1332 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8467 (t0) REVERT: B 130 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: B 207 GLU cc_start: 0.8283 (tp30) cc_final: 0.7523 (tt0) REVERT: B 279 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: B 321 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7525 (mmmt) REVERT: B 331 LYS cc_start: 0.9170 (mttp) cc_final: 0.8938 (mppt) REVERT: C 33 MET cc_start: 0.7516 (mtp) cc_final: 0.7256 (mtp) outliers start: 72 outliers final: 38 residues processed: 217 average time/residue: 0.5804 time to fit residues: 138.1322 Evaluate side-chains 204 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1230 SER Chi-restraints excluded: chain A residue 1232 SER Chi-restraints excluded: chain A residue 1289 GLU 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 92 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 279 GLN 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 B residue 377 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 43 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN A1442 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102343 restraints weight = 15609.195| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.13 r_work: 0.2928 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13539 Z= 0.174 Angle : 0.657 13.554 18361 Z= 0.327 Chirality : 0.047 0.181 2040 Planarity : 0.004 0.053 2350 Dihedral : 5.346 27.648 1798 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 4.36 % Allowed : 17.29 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1632 helix: -2.13 (0.46), residues: 104 sheet: -0.55 (0.20), residues: 633 loop : -1.85 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 404 TYR 0.019 0.002 TYR B 187 PHE 0.017 0.002 PHE A 16 TRP 0.017 0.002 TRP A1312 HIS 0.011 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00416 (13536) covalent geometry : angle 0.65666 (18361) hydrogen bonds : bond 0.03519 ( 340) hydrogen bonds : angle 5.48763 ( 906) metal coordination : bond 0.00593 ( 3) *********************** 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: 63 poor density : 166 time to evaluate : 0.523 Fit side-chains REVERT: A 199 LYS cc_start: 0.7141 (tmtt) cc_final: 0.6897 (tmtt) REVERT: A 237 THR cc_start: 0.8339 (p) cc_final: 0.7884 (p) REVERT: A 319 ARG cc_start: 0.8448 (ttt180) cc_final: 0.8245 (ttt180) REVERT: A 498 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8055 (pp) REVERT: A 633 ASN cc_start: 0.8412 (m-40) cc_final: 0.8086 (m-40) REVERT: A 982 ASN cc_start: 0.8050 (p0) cc_final: 0.7384 (m110) REVERT: A 1063 ASP cc_start: 0.7576 (t0) cc_final: 0.7311 (t0) REVERT: A 1112 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7170 (mp0) REVERT: A 1146 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: A 1186 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 1289 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: A 1294 MET cc_start: 0.8071 (ttm) cc_final: 0.7806 (mtp) REVERT: B 130 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: B 207 GLU cc_start: 0.8310 (tp30) cc_final: 0.7619 (tt0) REVERT: B 240 LEU cc_start: 0.8701 (mt) cc_final: 0.8316 (mt) REVERT: B 279 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: B 321 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7550 (mmmt) outliers start: 63 outliers final: 40 residues processed: 210 average time/residue: 0.6083 time to fit residues: 139.9158 Evaluate side-chains 198 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 119 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 590 GLN 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 790 GLU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1082 VAL Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1215 MET 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 92 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 279 GLN 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 B residue 377 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 HIS A1237 GLN A1332 ASN A1442 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.099865 restraints weight = 15538.348| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.12 r_work: 0.2968 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13539 Z= 0.171 Angle : 0.644 13.468 18361 Z= 0.322 Chirality : 0.047 0.179 2040 Planarity : 0.004 0.052 2350 Dihedral : 5.312 27.702 1798 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.72 % Favored : 92.22 % Rotamer: Outliers : 4.70 % Allowed : 17.70 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.20), residues: 1632 helix: -1.92 (0.48), residues: 105 sheet: -0.48 (0.20), residues: 640 loop : -1.80 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 616 TYR 0.021 0.002 TYR B 187 PHE 0.018 0.002 PHE A 16 TRP 0.017 0.002 TRP A1312 HIS 0.010 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00409 (13536) covalent geometry : angle 0.64435 (18361) hydrogen bonds : bond 0.03480 ( 340) hydrogen bonds : angle 5.42162 ( 906) metal coordination : bond 0.00504 ( 3) *********************** 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 226 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 0.366 Fit side-chains REVERT: A 199 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6897 (tmtt) REVERT: A 237 THR cc_start: 0.8394 (p) cc_final: 0.7947 (p) REVERT: A 319 ARG cc_start: 0.8485 (ttt180) cc_final: 0.8271 (ttt180) REVERT: A 378 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7299 (mt-10) REVERT: A 498 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8197 (pp) REVERT: A 580 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6818 (tt0) REVERT: A 594 GLU cc_start: 0.8310 (tt0) cc_final: 0.8026 (tt0) REVERT: A 633 ASN cc_start: 0.8450 (m-40) cc_final: 0.8159 (m-40) REVERT: A 982 ASN cc_start: 0.8081 (p0) cc_final: 0.7460 (m110) REVERT: A 996 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8729 (tm) REVERT: A 1063 ASP cc_start: 0.7665 (t0) cc_final: 0.7385 (t0) REVERT: A 1064 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: A 1112 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7205 (mp0) REVERT: A 1146 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: A 1186 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8488 (mt) REVERT: A 1289 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: A 1294 MET cc_start: 0.8027 (ttm) cc_final: 0.7756 (mtp) REVERT: B 130 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: B 207 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: B 240 LEU cc_start: 0.8699 (mt) cc_final: 0.8298 (mt) REVERT: B 279 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: B 321 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7565 (mmmt) outliers start: 68 outliers final: 39 residues processed: 203 average time/residue: 0.6312 time to fit residues: 139.6141 Evaluate side-chains 204 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 119 SER 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 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 620 GLN Chi-restraints excluded: chain A residue 642 LEU 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 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1215 MET 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 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 92 LEU Chi-restraints excluded: chain B residue 98 MET 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 247 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 chunk 84 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 866 HIS A1332 ASN A1442 HIS B 160 HIS B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101492 restraints weight = 15444.859| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.11 r_work: 0.2981 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13539 Z= 0.150 Angle : 0.628 13.379 18361 Z= 0.315 Chirality : 0.047 0.241 2040 Planarity : 0.004 0.051 2350 Dihedral : 5.225 27.641 1798 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 4.43 % Allowed : 18.33 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.20), residues: 1632 helix: -1.93 (0.47), residues: 111 sheet: -0.37 (0.20), residues: 636 loop : -1.77 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1274 TYR 0.016 0.001 TYR B 187 PHE 0.014 0.001 PHE A 16 TRP 0.017 0.002 TRP A1337 HIS 0.009 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00358 (13536) covalent geometry : angle 0.62825 (18361) hydrogen bonds : bond 0.03376 ( 340) hydrogen bonds : angle 5.40170 ( 906) metal coordination : bond 0.00466 ( 3) *********************** 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 220 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 156 time to evaluate : 0.559 Fit side-chains REVERT: A 124 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: A 199 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6929 (tmtt) REVERT: A 237 THR cc_start: 0.8392 (p) cc_final: 0.7934 (p) REVERT: A 319 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8219 (ttt180) REVERT: A 378 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7299 (mt-10) REVERT: A 498 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8224 (pp) REVERT: A 580 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6831 (tt0) REVERT: A 594 GLU cc_start: 0.8325 (tt0) cc_final: 0.8051 (tt0) REVERT: A 633 ASN cc_start: 0.8381 (m-40) cc_final: 0.8066 (m-40) REVERT: A 790 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 982 ASN cc_start: 0.8067 (p0) cc_final: 0.7446 (m110) REVERT: A 996 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8768 (tm) REVERT: A 1063 ASP cc_start: 0.7658 (t0) cc_final: 0.7363 (t0) REVERT: A 1064 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: A 1112 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7207 (mp0) REVERT: A 1146 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7313 (tp30) REVERT: A 1186 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8501 (mt) REVERT: A 1289 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 1294 MET cc_start: 0.7976 (ttm) cc_final: 0.7692 (mtp) REVERT: B 130 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: B 207 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: B 279 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8106 (pt0) REVERT: B 321 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7544 (mmmt) outliers start: 64 outliers final: 35 residues processed: 198 average time/residue: 0.6334 time to fit residues: 136.8007 Evaluate side-chains 200 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 119 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 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 790 GLU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1215 MET 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 92 LEU Chi-restraints excluded: chain B residue 98 MET 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 247 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 ASN A1442 HIS B 189 GLN B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100151 restraints weight = 15312.618| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.09 r_work: 0.2895 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13539 Z= 0.194 Angle : 0.672 13.510 18361 Z= 0.336 Chirality : 0.048 0.224 2040 Planarity : 0.005 0.053 2350 Dihedral : 5.387 28.122 1798 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.84 % Favored : 92.10 % Rotamer: Outliers : 4.22 % Allowed : 18.46 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.20), residues: 1632 helix: -1.93 (0.47), residues: 111 sheet: -0.39 (0.20), residues: 639 loop : -1.75 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1298 TYR 0.022 0.002 TYR B 187 PHE 0.018 0.002 PHE A 16 TRP 0.019 0.002 TRP A1312 HIS 0.011 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00468 (13536) covalent geometry : angle 0.67169 (18361) hydrogen bonds : bond 0.03547 ( 340) hydrogen bonds : angle 5.44408 ( 906) metal coordination : bond 0.00487 ( 3) *********************** 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 218 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 0.507 Fit side-chains REVERT: A 124 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: A 199 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7038 (tttt) REVERT: A 237 THR cc_start: 0.8477 (p) cc_final: 0.8045 (p) REVERT: A 319 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8223 (ttt180) REVERT: A 378 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7360 (mt-10) REVERT: A 498 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8234 (pp) REVERT: A 580 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6832 (tt0) REVERT: A 593 MET cc_start: 0.7776 (mmm) cc_final: 0.7525 (mmm) REVERT: A 594 GLU cc_start: 0.8365 (tt0) cc_final: 0.8112 (tt0) REVERT: A 633 ASN cc_start: 0.8417 (m-40) cc_final: 0.8112 (m-40) REVERT: A 790 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: A 982 ASN cc_start: 0.8129 (p0) cc_final: 0.7558 (m110) REVERT: A 1064 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 1112 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 1146 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: A 1186 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 1294 MET cc_start: 0.8095 (ttm) cc_final: 0.7833 (mtp) REVERT: B 130 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: B 207 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: B 279 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8068 (pt0) outliers start: 61 outliers final: 38 residues processed: 198 average time/residue: 0.6284 time to fit residues: 135.4249 Evaluate side-chains 198 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 119 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 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 620 GLN Chi-restraints excluded: chain A residue 642 LEU 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 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1064 GLU Chi-restraints excluded: chain A residue 1146 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 1242 THR 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 92 LEU Chi-restraints excluded: chain B residue 98 MET 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 247 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 155 optimal weight: 0.0470 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101679 restraints weight = 15499.608| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.10 r_work: 0.2971 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13539 Z= 0.151 Angle : 0.636 13.292 18361 Z= 0.317 Chirality : 0.047 0.217 2040 Planarity : 0.004 0.050 2350 Dihedral : 5.261 28.033 1798 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 3.67 % Allowed : 19.29 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1632 helix: -1.74 (0.48), residues: 111 sheet: -0.31 (0.20), residues: 642 loop : -1.75 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.016 0.001 TYR B 187 PHE 0.014 0.002 PHE B 217 TRP 0.018 0.002 TRP A1337 HIS 0.009 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00358 (13536) covalent geometry : angle 0.63648 (18361) hydrogen bonds : bond 0.03343 ( 340) hydrogen bonds : angle 5.38290 ( 906) metal coordination : bond 0.00451 ( 3) *********************** 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 205 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 0.532 Fit side-chains REVERT: A 124 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: A 199 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7107 (tmtt) REVERT: A 237 THR cc_start: 0.8444 (p) cc_final: 0.8023 (p) REVERT: A 319 ARG cc_start: 0.8433 (ttt180) cc_final: 0.8205 (ttt180) REVERT: A 378 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7356 (mt-10) REVERT: A 498 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8247 (pp) REVERT: A 580 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6825 (tt0) REVERT: A 593 MET cc_start: 0.7786 (mmm) cc_final: 0.7544 (mmm) REVERT: A 594 GLU cc_start: 0.8347 (tt0) cc_final: 0.8050 (tt0) REVERT: A 633 ASN cc_start: 0.8381 (m-40) cc_final: 0.8077 (m-40) REVERT: A 982 ASN cc_start: 0.8100 (p0) cc_final: 0.7515 (m110) REVERT: A 1112 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7214 (mp0) REVERT: A 1146 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7351 (tp30) REVERT: A 1186 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 1294 MET cc_start: 0.7924 (ttm) cc_final: 0.7641 (mtp) REVERT: B 130 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: B 207 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: B 279 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8109 (pt0) REVERT: B 321 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7435 (mmmt) outliers start: 53 outliers final: 33 residues processed: 187 average time/residue: 0.6371 time to fit residues: 129.9599 Evaluate side-chains 191 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 119 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 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 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1146 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 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 92 LEU Chi-restraints excluded: chain B residue 98 MET 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 247 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain F residue 486 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 94 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101593 restraints weight = 15471.733| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.09 r_work: 0.2981 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3962 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= 0.156 Angle : 0.639 13.216 18361 Z= 0.318 Chirality : 0.047 0.214 2040 Planarity : 0.004 0.051 2350 Dihedral : 5.226 27.889 1798 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.84 % Favored : 92.10 % Rotamer: Outliers : 3.18 % Allowed : 19.92 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.20), residues: 1632 helix: -1.65 (0.48), residues: 111 sheet: -0.27 (0.20), residues: 641 loop : -1.73 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 148 TYR 0.017 0.001 TYR B 187 PHE 0.015 0.002 PHE A 16 TRP 0.018 0.002 TRP A1337 HIS 0.009 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00372 (13536) covalent geometry : angle 0.63857 (18361) hydrogen bonds : bond 0.03342 ( 340) hydrogen bonds : angle 5.33132 ( 906) metal coordination : bond 0.00482 ( 3) ********************** 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 200 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.572 Fit side-chains REVERT: A 124 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: A 199 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7136 (tmtt) REVERT: A 237 THR cc_start: 0.8464 (p) cc_final: 0.8038 (p) REVERT: A 319 ARG cc_start: 0.8439 (ttt180) cc_final: 0.8201 (ttt180) REVERT: A 378 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7213 (mt-10) REVERT: A 498 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8249 (pp) REVERT: A 580 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6838 (tt0) REVERT: A 593 MET cc_start: 0.7779 (mmm) cc_final: 0.7526 (mmm) REVERT: A 594 GLU cc_start: 0.8339 (tt0) cc_final: 0.8061 (tt0) REVERT: A 633 ASN cc_start: 0.8365 (m-40) cc_final: 0.8043 (m-40) REVERT: A 982 ASN cc_start: 0.8097 (p0) cc_final: 0.7505 (m110) REVERT: A 1112 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7241 (mp0) REVERT: A 1146 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7339 (tp30) REVERT: A 1186 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8507 (mt) REVERT: A 1294 MET cc_start: 0.7936 (ttm) cc_final: 0.7663 (mtp) REVERT: B 130 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7884 (pm20) REVERT: B 207 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: B 279 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (pt0) outliers start: 46 outliers final: 34 residues processed: 187 average time/residue: 0.5855 time to fit residues: 119.7576 Evaluate side-chains 191 residues out of total 1446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 119 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 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 620 GLN Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1146 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 92 LEU Chi-restraints excluded: chain B residue 98 MET 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 247 VAL Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 LEU 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 125 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 153 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 268 GLN B 319 ASN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098678 restraints weight = 15359.845| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.07 r_work: 0.2939 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13539 Z= 0.219 Angle : 0.705 13.464 18361 Z= 0.350 Chirality : 0.049 0.227 2040 Planarity : 0.005 0.056 2350 Dihedral : 5.481 28.818 1798 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.15 % Favored : 91.79 % Rotamer: Outliers : 3.32 % Allowed : 20.12 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.20), residues: 1632 helix: -1.81 (0.48), residues: 111 sheet: -0.38 (0.20), residues: 648 loop : -1.71 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1298 TYR 0.024 0.002 TYR B 187 PHE 0.019 0.002 PHE A1443 TRP 0.023 0.002 TRP A1312 HIS 0.012 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00530 (13536) covalent geometry : angle 0.70495 (18361) hydrogen bonds : bond 0.03636 ( 340) hydrogen bonds : angle 5.44216 ( 906) metal coordination : bond 0.00599 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4488.91 seconds wall clock time: 77 minutes 18.87 seconds (4638.87 seconds total)