Starting phenix.real_space_refine on Thu Jan 16 09:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v81_43014/01_2025/8v81_43014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v81_43014/01_2025/8v81_43014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v81_43014/01_2025/8v81_43014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v81_43014/01_2025/8v81_43014.map" model { file = "/net/cci-nas-00/data/ceres_data/8v81_43014/01_2025/8v81_43014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v81_43014/01_2025/8v81_43014.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6065 2.51 5 N 1518 2.21 5 O 1616 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9258 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 9085 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 32, 'TRANS': 1099} Chain breaks: 5 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 173 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'POV': 5, 'WG5': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 58 Time building chain proxies: 6.11, per 1000 atoms: 0.66 Number of scatterers: 9258 At special positions: 0 Unit cell: (116.521, 93.003, 120.797, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 48 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1616 8.00 N 1518 7.00 C 6065 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 63.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.686A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 50 through 64 removed outlier: 3.664A pdb=" N ARG A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 75 removed outlier: 4.132A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 94 removed outlier: 3.883A pdb=" N THR A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 removed outlier: 3.540A pdb=" N ALA A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 165 removed outlier: 3.995A pdb=" N ILE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N CYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 132 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.723A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.681A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 202 removed outlier: 3.656A pdb=" N HIS A 199 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP A 202 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.771A pdb=" N GLU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 removed outlier: 3.683A pdb=" N ARG A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 268 removed outlier: 4.351A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.580A pdb=" N VAL A 272 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 308 removed outlier: 3.787A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 285 " --> pdb=" O MET A 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 330 Proline residue: A 324 - end of helix removed outlier: 3.722A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.544A pdb=" N THR A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 501 through 508 Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 526 through 533 removed outlier: 3.746A pdb=" N ILE A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.848A pdb=" N ARG A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.578A pdb=" N GLU A 588 " --> pdb=" O LYS A 584 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.748A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.724A pdb=" N GLN A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 854 removed outlier: 3.617A pdb=" N THR A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 removed outlier: 3.960A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 869 " --> pdb=" O TRP A 865 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE A 870 " --> pdb=" O CYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 4.038A pdb=" N TRP A 882 " --> pdb=" O VAL A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 922 removed outlier: 3.598A pdb=" N VAL A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 934 through 958 removed outlier: 3.536A pdb=" N ILE A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 943 " --> pdb=" O HIS A 939 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 removed outlier: 3.953A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 967 " --> pdb=" O THR A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 977 removed outlier: 3.600A pdb=" N SER A 977 " --> pdb=" O LEU A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 986 removed outlier: 3.513A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1012 removed outlier: 4.240A pdb=" N VAL A1007 " --> pdb=" O GLY A1003 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A1012 " --> pdb=" O VAL A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1047 removed outlier: 3.705A pdb=" N VAL A1022 " --> pdb=" O ALA A1018 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1043 " --> pdb=" O GLN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.938A pdb=" N PHE A1052 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1067 removed outlier: 3.594A pdb=" N ARG A1066 " --> pdb=" O LEU A1062 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A1067 " --> pdb=" O TRP A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1120 removed outlier: 3.982A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A1092 " --> pdb=" O ASN A1088 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA A1113 " --> pdb=" O ILE A1109 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A1114 " --> pdb=" O PHE A1110 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A1116 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A1118 " --> pdb=" O VAL A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1168 removed outlier: 3.770A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1259 removed outlier: 3.596A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 removed outlier: 3.655A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1323 removed outlier: 3.521A pdb=" N VAL A1318 " --> pdb=" O GLU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1329 removed outlier: 3.522A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 3.791A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A1353 " --> pdb=" O GLY A1349 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1392 removed outlier: 3.608A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A1390 " --> pdb=" O ARG A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1440 Processing sheet with id=AA1, first strand: chain 'A' and resid 441 through 448 removed outlier: 6.616A pdb=" N LYS A 442 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 398 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN A 396 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 3.629A pdb=" N CYS A 491 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 454 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 626 " --> pdb=" O ILE A 618 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1227 through 1234 removed outlier: 6.922A pdb=" N GLU A1228 " --> pdb=" O THR A1216 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A1216 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE A1232 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A1234 " --> pdb=" O MET A1210 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A1266 " --> pdb=" O LYS A1213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 7.470A pdb=" N LEU A1367 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY A1241 " --> pdb=" O LEU A1414 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A1416 " --> pdb=" O GLY A1241 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A1243 " --> pdb=" O ILE A1416 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2837 1.34 - 1.46: 1998 1.46 - 1.58: 4531 1.58 - 1.70: 9 1.70 - 1.81: 79 Bond restraints: 9454 Sorted by residual: bond pdb=" C22 WG5 A1511 " pdb=" S23 WG5 A1511 " ideal model delta sigma weight residual 1.631 1.657 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" CB PHE A1107 " pdb=" CG PHE A1107 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.30e-02 1.89e+03 1.23e+00 bond pdb=" C LEU A 987 " pdb=" N PRO A 988 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 bond pdb=" C15 WG5 A1511 " pdb=" C18 WG5 A1511 " ideal model delta sigma weight residual 1.529 1.509 0.020 2.00e-02 2.50e+03 9.79e-01 bond pdb=" C8 WG5 A1511 " pdb=" O9 WG5 A1511 " ideal model delta sigma weight residual 1.204 1.224 -0.020 2.00e-02 2.50e+03 9.78e-01 ... (remaining 9449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 12609 1.71 - 3.42: 137 3.42 - 5.14: 25 5.14 - 6.85: 8 6.85 - 8.56: 5 Bond angle restraints: 12784 Sorted by residual: angle pdb=" C PRO A 111 " pdb=" N ASP A 112 " pdb=" CA ASP A 112 " ideal model delta sigma weight residual 122.68 126.81 -4.13 1.47e+00 4.63e-01 7.88e+00 angle pdb=" CB MET A 82 " pdb=" CG MET A 82 " pdb=" SD MET A 82 " ideal model delta sigma weight residual 112.70 120.59 -7.89 3.00e+00 1.11e-01 6.93e+00 angle pdb=" C THR A 382 " pdb=" N LEU A 383 " pdb=" CA LEU A 383 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" CA LEU A 570 " pdb=" CB LEU A 570 " pdb=" CG LEU A 570 " ideal model delta sigma weight residual 116.30 124.86 -8.56 3.50e+00 8.16e-02 5.98e+00 angle pdb=" CB MET A 244 " pdb=" CG MET A 244 " pdb=" SD MET A 244 " ideal model delta sigma weight residual 112.70 119.67 -6.97 3.00e+00 1.11e-01 5.40e+00 ... (remaining 12779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4669 17.71 - 35.41: 743 35.41 - 53.11: 239 53.11 - 70.82: 60 70.82 - 88.52: 12 Dihedral angle restraints: 5723 sinusoidal: 2434 harmonic: 3289 Sorted by residual: dihedral pdb=" CA ASP A 112 " pdb=" C ASP A 112 " pdb=" N ASN A 113 " pdb=" CA ASN A 113 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP A 192 " pdb=" CB ASP A 192 " pdb=" CG ASP A 192 " pdb=" OD1 ASP A 192 " ideal model delta sinusoidal sigma weight residual -30.00 -89.10 59.10 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA GLU A 535 " pdb=" C GLU A 535 " pdb=" N LYS A 536 " pdb=" CA LYS A 536 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 5720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 869 0.028 - 0.056: 393 0.056 - 0.084: 148 0.084 - 0.111: 42 0.111 - 0.139: 15 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CA PRO A 499 " pdb=" N PRO A 499 " pdb=" C PRO A 499 " pdb=" CB PRO A 499 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A1295 " pdb=" N ILE A1295 " pdb=" C ILE A1295 " pdb=" CB ILE A1295 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE A 482 " pdb=" N ILE A 482 " pdb=" C ILE A 482 " pdb=" CB ILE A 482 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1464 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1049 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A1050 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A1050 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1050 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 98 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 99 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1235 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A1236 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1236 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1236 " 0.030 5.00e-02 4.00e+02 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 51 2.57 - 3.16: 6990 3.16 - 3.74: 13939 3.74 - 4.32: 18011 4.32 - 4.90: 31479 Nonbonded interactions: 70470 Sorted by model distance: nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 1.993 2.170 nonbonded pdb=" OE1 GLN A1291 " pdb="MG MG A1502 " model vdw 1.994 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.018 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.063 2.170 nonbonded pdb=" OD1 ASN A 189 " pdb=" NH2 ARG A1048 " model vdw 2.235 3.120 ... (remaining 70465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.003 0.031 9454 Z= 0.178 Angle : 0.532 8.562 12784 Z= 0.267 Chirality : 0.038 0.139 1467 Planarity : 0.004 0.058 1549 Dihedral : 19.319 88.522 3595 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.50 % Allowed : 36.92 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.25), residues: 1120 helix: 0.36 (0.21), residues: 683 sheet: -1.95 (0.65), residues: 65 loop : -1.68 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1063 HIS 0.002 0.001 HIS A 949 PHE 0.019 0.001 PHE A1166 TYR 0.013 0.001 TYR A1073 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 0.857 Fit side-chains REVERT: A 267 GLU cc_start: 0.6764 (tp30) cc_final: 0.6463 (mt-10) REVERT: A 635 ASN cc_start: 0.6397 (m-40) cc_final: 0.6187 (m110) REVERT: A 1110 PHE cc_start: 0.5576 (m-80) cc_final: 0.5357 (m-80) outliers start: 5 outliers final: 4 residues processed: 123 average time/residue: 0.2149 time to fit residues: 38.0057 Evaluate side-chains 122 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 1272 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.131239 restraints weight = 10518.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.131358 restraints weight = 9561.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132258 restraints weight = 8584.627| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9454 Z= 0.197 Angle : 0.509 10.757 12784 Z= 0.257 Chirality : 0.038 0.153 1467 Planarity : 0.004 0.055 1549 Dihedral : 8.345 83.417 1424 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.53 % Allowed : 33.90 % Favored : 60.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1120 helix: 0.50 (0.21), residues: 675 sheet: -1.21 (0.56), residues: 80 loop : -1.71 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1063 HIS 0.002 0.001 HIS A 949 PHE 0.015 0.001 PHE A1166 TYR 0.013 0.001 TYR A1073 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.878 Fit side-chains REVERT: A 116 GLU cc_start: 0.0612 (OUTLIER) cc_final: -0.1074 (pt0) REVERT: A 244 MET cc_start: 0.8647 (tmm) cc_final: 0.8343 (tmm) REVERT: A 270 GLN cc_start: 0.7629 (tt0) cc_final: 0.7339 (tt0) REVERT: A 288 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8022 (mt) REVERT: A 329 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5981 (tmtt) REVERT: A 375 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 635 ASN cc_start: 0.6213 (m-40) cc_final: 0.5911 (m110) REVERT: A 1065 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8370 (mp) REVERT: A 1110 PHE cc_start: 0.5525 (m-80) cc_final: 0.5305 (m-80) REVERT: A 1154 ASP cc_start: 0.7619 (t0) cc_final: 0.7327 (m-30) outliers start: 55 outliers final: 24 residues processed: 173 average time/residue: 0.1999 time to fit residues: 49.1591 Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.145461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130114 restraints weight = 10563.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.130191 restraints weight = 10166.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130808 restraints weight = 9072.292| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9454 Z= 0.211 Angle : 0.512 8.149 12784 Z= 0.258 Chirality : 0.039 0.168 1467 Planarity : 0.004 0.054 1549 Dihedral : 7.177 74.936 1420 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.84 % Allowed : 32.70 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1120 helix: 0.59 (0.21), residues: 668 sheet: -1.23 (0.54), residues: 80 loop : -1.67 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1063 HIS 0.003 0.001 HIS A 949 PHE 0.015 0.001 PHE A 81 TYR 0.014 0.001 TYR A1073 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 1.001 Fit side-chains REVERT: A 116 GLU cc_start: 0.0686 (OUTLIER) cc_final: -0.1042 (pt0) REVERT: A 268 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8583 (p0) REVERT: A 270 GLN cc_start: 0.7576 (tt0) cc_final: 0.7365 (tt0) REVERT: A 288 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8073 (mt) REVERT: A 329 LYS cc_start: 0.6497 (OUTLIER) cc_final: 0.6114 (tmtt) REVERT: A 375 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8077 (mp) REVERT: A 1065 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 1154 ASP cc_start: 0.7706 (t0) cc_final: 0.7429 (m-30) outliers start: 68 outliers final: 39 residues processed: 180 average time/residue: 0.1908 time to fit residues: 49.8382 Evaluate side-chains 167 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1139 ILE Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1431 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 80 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 359 GLN A 635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.146591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.130888 restraints weight = 10534.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132140 restraints weight = 8230.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133303 restraints weight = 6897.442| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9454 Z= 0.173 Angle : 0.487 7.673 12784 Z= 0.246 Chirality : 0.038 0.152 1467 Planarity : 0.003 0.053 1549 Dihedral : 6.755 76.684 1420 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.74 % Allowed : 33.50 % Favored : 59.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1120 helix: 0.65 (0.21), residues: 679 sheet: -1.15 (0.54), residues: 80 loop : -1.67 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1063 HIS 0.002 0.001 HIS A 949 PHE 0.013 0.001 PHE A 81 TYR 0.012 0.001 TYR A1073 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 127 time to evaluate : 0.997 Fit side-chains REVERT: A 116 GLU cc_start: 0.0420 (OUTLIER) cc_final: -0.1200 (pt0) REVERT: A 270 GLN cc_start: 0.7570 (tt0) cc_final: 0.7332 (tt0) REVERT: A 288 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7976 (mt) REVERT: A 329 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6074 (tmtt) REVERT: A 375 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 1065 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8324 (mp) REVERT: A 1154 ASP cc_start: 0.7659 (t0) cc_final: 0.7352 (m-30) REVERT: A 1166 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.6853 (t80) outliers start: 67 outliers final: 43 residues processed: 183 average time/residue: 0.1926 time to fit residues: 50.8923 Evaluate side-chains 175 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 268 ASN A 635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.141863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.125842 restraints weight = 10740.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.127164 restraints weight = 8418.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128319 restraints weight = 7077.435| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9454 Z= 0.318 Angle : 0.580 8.035 12784 Z= 0.294 Chirality : 0.041 0.166 1467 Planarity : 0.004 0.054 1549 Dihedral : 7.148 67.375 1420 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 8.25 % Allowed : 32.60 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1120 helix: 0.36 (0.21), residues: 673 sheet: -1.65 (0.59), residues: 70 loop : -1.77 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1063 HIS 0.004 0.001 HIS A 949 PHE 0.019 0.002 PHE A 446 TYR 0.017 0.002 TYR A1073 ARG 0.002 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 122 time to evaluate : 0.915 Fit side-chains REVERT: A 49 LEU cc_start: 0.8266 (tp) cc_final: 0.7968 (tp) REVERT: A 116 GLU cc_start: 0.0253 (OUTLIER) cc_final: -0.1783 (pm20) REVERT: A 270 GLN cc_start: 0.7560 (tt0) cc_final: 0.7337 (tt0) REVERT: A 329 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6311 (tmtt) REVERT: A 537 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: A 1063 TRP cc_start: 0.7924 (m-10) cc_final: 0.7465 (m-10) REVERT: A 1166 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 1437 PHE cc_start: 0.2572 (OUTLIER) cc_final: 0.2132 (t80) outliers start: 82 outliers final: 55 residues processed: 188 average time/residue: 0.1872 time to fit residues: 51.0541 Evaluate side-chains 179 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 119 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1150 SER Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1395 CYS Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1427 ILE Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.144813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.130112 restraints weight = 10545.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.129756 restraints weight = 10953.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.130863 restraints weight = 9676.264| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9454 Z= 0.208 Angle : 0.511 6.765 12784 Z= 0.258 Chirality : 0.039 0.141 1467 Planarity : 0.003 0.053 1549 Dihedral : 6.710 66.686 1420 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 7.75 % Allowed : 33.00 % Favored : 59.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1120 helix: 0.52 (0.21), residues: 677 sheet: -1.39 (0.55), residues: 80 loop : -1.79 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1063 HIS 0.003 0.001 HIS A 949 PHE 0.013 0.001 PHE A 446 TYR 0.013 0.001 TYR A1073 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 122 time to evaluate : 1.027 Fit side-chains REVERT: A 116 GLU cc_start: 0.0778 (OUTLIER) cc_final: -0.0918 (pt0) REVERT: A 170 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6574 (mtt-85) REVERT: A 268 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8764 (p0) REVERT: A 288 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8086 (mt) REVERT: A 329 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6240 (tmtt) REVERT: A 537 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: A 883 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4599 (tp) REVERT: A 1063 TRP cc_start: 0.7913 (m-10) cc_final: 0.7476 (m-10) REVERT: A 1166 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6888 (t80) REVERT: A 1437 PHE cc_start: 0.2672 (OUTLIER) cc_final: 0.1916 (t80) outliers start: 77 outliers final: 54 residues processed: 186 average time/residue: 0.1951 time to fit residues: 52.5869 Evaluate side-chains 185 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1274 TRP Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.144213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.129137 restraints weight = 10614.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129329 restraints weight = 9363.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.129978 restraints weight = 8262.013| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9454 Z= 0.227 Angle : 0.525 7.061 12784 Z= 0.263 Chirality : 0.039 0.144 1467 Planarity : 0.003 0.052 1549 Dihedral : 6.734 65.281 1420 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 8.65 % Allowed : 32.29 % Favored : 59.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1120 helix: 0.48 (0.21), residues: 683 sheet: -1.40 (0.55), residues: 80 loop : -1.78 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 865 HIS 0.003 0.001 HIS A 949 PHE 0.014 0.001 PHE A 446 TYR 0.013 0.001 TYR A1073 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 123 time to evaluate : 0.944 Fit side-chains REVERT: A 116 GLU cc_start: 0.0597 (OUTLIER) cc_final: -0.1053 (pt0) REVERT: A 170 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6541 (mtt-85) REVERT: A 268 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8671 (p0) REVERT: A 288 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 329 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.6173 (tmtt) REVERT: A 378 GLN cc_start: 0.8179 (tt0) cc_final: 0.7947 (tt0) REVERT: A 384 GLU cc_start: 0.4636 (OUTLIER) cc_final: 0.4382 (pm20) REVERT: A 537 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: A 1063 TRP cc_start: 0.7936 (m-10) cc_final: 0.7485 (m-10) REVERT: A 1166 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.6813 (t80) REVERT: A 1437 PHE cc_start: 0.2564 (OUTLIER) cc_final: 0.1618 (t80) outliers start: 86 outliers final: 64 residues processed: 194 average time/residue: 0.1924 time to fit residues: 53.9421 Evaluate side-chains 196 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 123 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1150 SER Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1163 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1274 TRP Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1288 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1395 CYS Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.145864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.130357 restraints weight = 10690.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.131668 restraints weight = 8351.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.132840 restraints weight = 6982.675| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9454 Z= 0.175 Angle : 0.498 8.345 12784 Z= 0.249 Chirality : 0.038 0.140 1467 Planarity : 0.003 0.052 1549 Dihedral : 6.470 64.316 1420 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 7.34 % Allowed : 33.50 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1120 helix: 0.62 (0.21), residues: 685 sheet: -1.56 (0.52), residues: 87 loop : -1.68 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 865 HIS 0.002 0.001 HIS A1375 PHE 0.012 0.001 PHE A 81 TYR 0.011 0.001 TYR A1073 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 129 time to evaluate : 0.934 Fit side-chains REVERT: A 116 GLU cc_start: 0.0493 (OUTLIER) cc_final: -0.0700 (pt0) REVERT: A 288 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8067 (mt) REVERT: A 384 GLU cc_start: 0.4599 (OUTLIER) cc_final: 0.4329 (pm20) REVERT: A 512 TYR cc_start: 0.7600 (t80) cc_final: 0.7041 (t80) REVERT: A 516 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7634 (ttt90) REVERT: A 537 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: A 1063 TRP cc_start: 0.7906 (m-10) cc_final: 0.7514 (m-10) REVERT: A 1166 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6881 (t80) REVERT: A 1437 PHE cc_start: 0.2584 (OUTLIER) cc_final: 0.1554 (t80) outliers start: 73 outliers final: 53 residues processed: 191 average time/residue: 0.2071 time to fit residues: 56.0708 Evaluate side-chains 186 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 126 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1395 CYS Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129035 restraints weight = 10545.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130388 restraints weight = 8328.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.131309 restraints weight = 6957.207| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9454 Z= 0.217 Angle : 0.534 11.038 12784 Z= 0.264 Chirality : 0.039 0.167 1467 Planarity : 0.003 0.051 1549 Dihedral : 6.573 63.178 1420 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 7.44 % Allowed : 33.40 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1120 helix: 0.58 (0.21), residues: 683 sheet: -1.37 (0.54), residues: 80 loop : -1.72 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1274 HIS 0.003 0.001 HIS A 949 PHE 0.014 0.001 PHE A 81 TYR 0.012 0.001 TYR A1073 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 122 time to evaluate : 1.028 Fit side-chains REVERT: A 116 GLU cc_start: 0.0315 (OUTLIER) cc_final: -0.0939 (pt0) REVERT: A 268 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8697 (p0) REVERT: A 288 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 384 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.4296 (pm20) REVERT: A 512 TYR cc_start: 0.7648 (t80) cc_final: 0.7070 (t80) REVERT: A 516 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7617 (ttt90) REVERT: A 537 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: A 1063 TRP cc_start: 0.7960 (m-10) cc_final: 0.7511 (m-10) REVERT: A 1166 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.6827 (t80) REVERT: A 1437 PHE cc_start: 0.2635 (OUTLIER) cc_final: 0.1585 (t80) outliers start: 74 outliers final: 60 residues processed: 183 average time/residue: 0.1956 time to fit residues: 52.1523 Evaluate side-chains 189 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1150 SER Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1395 CYS Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 51 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.146860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131448 restraints weight = 10667.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131932 restraints weight = 9195.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132766 restraints weight = 8032.103| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9454 Z= 0.161 Angle : 0.498 8.962 12784 Z= 0.248 Chirality : 0.038 0.161 1467 Planarity : 0.003 0.052 1549 Dihedral : 6.280 62.320 1420 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 7.04 % Allowed : 33.60 % Favored : 59.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1120 helix: 0.75 (0.21), residues: 683 sheet: -1.46 (0.52), residues: 87 loop : -1.56 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1274 HIS 0.002 0.001 HIS A1375 PHE 0.011 0.001 PHE A 81 TYR 0.010 0.001 TYR A 849 ARG 0.002 0.000 ARG A1102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 127 time to evaluate : 1.035 Fit side-chains REVERT: A 116 GLU cc_start: 0.0296 (OUTLIER) cc_final: -0.0708 (pt0) REVERT: A 268 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8740 (p0) REVERT: A 288 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 384 GLU cc_start: 0.4693 (OUTLIER) cc_final: 0.4448 (pm20) REVERT: A 512 TYR cc_start: 0.7589 (t80) cc_final: 0.6926 (t80) REVERT: A 537 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: A 1063 TRP cc_start: 0.7905 (m-10) cc_final: 0.7508 (m-10) REVERT: A 1166 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7078 (t80) REVERT: A 1437 PHE cc_start: 0.2729 (OUTLIER) cc_final: 0.1733 (t80) outliers start: 70 outliers final: 57 residues processed: 187 average time/residue: 0.1868 time to fit residues: 51.1415 Evaluate side-chains 190 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1105 MET Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1150 SER Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1274 TRP Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1355 CYS Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1395 CYS Chi-restraints excluded: chain A residue 1404 ILE Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1437 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.146303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132127 restraints weight = 10591.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.131749 restraints weight = 10877.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132554 restraints weight = 9261.904| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 9454 Z= 0.236 Angle : 0.840 59.183 12784 Z= 0.480 Chirality : 0.040 0.366 1467 Planarity : 0.004 0.086 1549 Dihedral : 6.312 62.173 1420 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 6.84 % Allowed : 34.10 % Favored : 59.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1120 helix: 0.72 (0.21), residues: 684 sheet: -1.45 (0.52), residues: 87 loop : -1.55 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1274 HIS 0.002 0.001 HIS A 949 PHE 0.016 0.001 PHE A 374 TYR 0.011 0.001 TYR A 849 ARG 0.003 0.000 ARG A1102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.84 seconds wall clock time: 50 minutes 7.33 seconds (3007.33 seconds total)