Starting phenix.real_space_refine on Thu Feb 15 12:51:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bly_7113/02_2024/6bly_7113.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bly_7113/02_2024/6bly_7113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bly_7113/02_2024/6bly_7113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bly_7113/02_2024/6bly_7113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bly_7113/02_2024/6bly_7113.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bly_7113/02_2024/6bly_7113.pdb" } resolution = 3.36 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= 0.014 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7853 2.51 5 N 2132 2.21 5 O 2204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 702": "NH1" <-> "NH2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1274": "NH1" <-> "NH2" Residue "A ASP 1275": "OD1" <-> "OD2" Residue "A PHE 1338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12263 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9337 Classifications: {'peptide': 1177} Link IDs: {'PTRANS': 66, 'TRANS': 1110} Chain breaks: 12 Chain: "B" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2926 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 15, 'TRANS': 347} Time building chain proxies: 6.52, per 1000 atoms: 0.53 Number of scatterers: 12263 At special positions: 0 Unit cell: (88.81, 136.96, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2204 8.00 N 2132 7.00 C 7853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 2.3 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 35 sheets defined 6.4% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.747A pdb=" N GLN A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 1154 through 1156 No H-bonds generated for 'chain 'A' and resid 1154 through 1156' Processing helix chain 'A' and resid 1352 through 1369 removed outlier: 3.863A pdb=" N ARG A1358 " --> pdb=" O LYS A1354 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1359 " --> pdb=" O THR A1355 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A1361 " --> pdb=" O ARG A1357 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A1365 " --> pdb=" O MET A1361 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1376 removed outlier: 3.518A pdb=" N GLY A1375 " --> pdb=" O HIS A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1382 removed outlier: 3.677A pdb=" N ARG A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 removed outlier: 3.529A pdb=" N LEU A1408 " --> pdb=" O ASN A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1423 removed outlier: 3.588A pdb=" N SER A1416 " --> pdb=" O THR A1412 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A1418 " --> pdb=" O GLU A1414 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A1419 " --> pdb=" O ARG A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 removed outlier: 3.577A pdb=" N ILE A1429 " --> pdb=" O THR A1425 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A1431 " --> pdb=" O ASP A1427 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A1435 " --> pdb=" O ASP A1431 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR A1436 " --> pdb=" O ASP A1432 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 70 removed outlier: 3.734A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.835A pdb=" N LEU B 92 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.607A pdb=" N ASN B 104 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 106 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1312 through 1314 removed outlier: 6.187A pdb=" N ILE A1345 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 20 removed outlier: 3.888A pdb=" N GLN A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 38 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 71 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 40 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.637A pdb=" N ALA A 93 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 120 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 105 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.602A pdb=" N ARG A 140 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 189 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 208 removed outlier: 5.392A pdb=" N ILE A 203 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 222 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 205 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N CYS A 238 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 260 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 242 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP A 256 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A 244 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 254 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 270 removed outlier: 4.644A pdb=" N GLN A 267 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLY A 297 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.880A pdb=" N THR A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N PHE A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE A 350 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 329 removed outlier: 4.666A pdb=" N ILE A 344 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.641A pdb=" N LEU A 392 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 526 removed outlier: 5.368A pdb=" N VAL A 523 " --> pdb=" O VAL A1000 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A1000 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR A 525 " --> pdb=" O ILE A 998 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 989 " --> pdb=" O ARG A 997 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.666A pdb=" N ASP A 534 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 578 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.539A pdb=" N PHE A 608 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 646 through 651 removed outlier: 7.583A pdb=" N MET A 659 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N CYS A 649 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 657 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AB7, first strand: chain 'A' and resid 695 through 702 removed outlier: 3.620A pdb=" N THR A 697 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N MET A 794 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU A 807 " --> pdb=" O MET A 794 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 796 " --> pdb=" O VAL A 805 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 846 through 854 removed outlier: 6.529A pdb=" N HIS A 866 " --> pdb=" O LYS A 847 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 849 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 864 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 851 " --> pdb=" O TYR A 862 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A 862 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA A 853 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG A 860 " --> pdb=" O ALA A 853 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 872 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE A 873 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AC1, first strand: chain 'A' and resid 931 through 937 removed outlier: 5.645A pdb=" N TYR A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N SER A 941 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 955 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1021 through 1024 removed outlier: 6.598A pdb=" N ALA A1037 " --> pdb=" O HIS A1023 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1027 through 1028 Processing sheet with id=AC4, first strand: chain 'A' and resid 1046 through 1050 removed outlier: 3.544A pdb=" N GLU A1056 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1098 through 1106 removed outlier: 6.627A pdb=" N GLY A1124 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N MET A1103 " --> pdb=" O ALA A1122 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA A1122 " --> pdb=" O MET A1103 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A1105 " --> pdb=" O TYR A1120 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR A1120 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY A1137 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A1167 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A1139 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A1165 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A1141 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1172 through 1177 removed outlier: 4.104A pdb=" N ALA A1174 " --> pdb=" O ALA A1185 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A1192 " --> pdb=" O MET A1203 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1212 through 1217 removed outlier: 3.630A pdb=" N GLN A1214 " --> pdb=" O ALA A1225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1232 through 1237 removed outlier: 7.106A pdb=" N LEU A1233 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A1242 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.802A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 6.802A pdb=" N SER A1272 " --> pdb=" O TYR A1256 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1258 " --> pdb=" O LEU A1270 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A1270 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A1278 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP A1301 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A1280 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1297 " --> pdb=" O MET A1282 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.656A pdb=" N PHE B 401 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR B 113 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER B 399 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ILE B 389 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TRP B 383 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N CYS B 391 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B 381 " --> pdb=" O CYS B 391 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLY B 393 " --> pdb=" O TRP B 379 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.575A pdb=" N ARG B 126 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 135 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 164 through 169 removed outlier: 4.072A pdb=" N ALA B 166 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N TYR B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 187 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS B 196 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN B 189 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B 194 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 205 through 210 removed outlier: 6.895A pdb=" N CYS B 220 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B 208 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 218 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE B 210 " --> pdb=" O LYS B 216 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS B 216 " --> pdb=" O PHE B 210 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 226 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 239 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 228 " --> pdb=" O GLU B 237 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AD7, first strand: chain 'B' and resid 291 through 296 Processing sheet with id=AD8, first strand: chain 'B' and resid 334 through 339 removed outlier: 3.929A pdb=" N ALA B 336 " --> pdb=" O GLY B 350 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3252 1.33 - 1.45: 2273 1.45 - 1.57: 6918 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 12563 Sorted by residual: bond pdb=" C PHE A 811 " pdb=" N PRO A 812 " ideal model delta sigma weight residual 1.337 1.384 -0.047 9.80e-03 1.04e+04 2.32e+01 bond pdb=" CA LEU A 201 " pdb=" C LEU A 201 " ideal model delta sigma weight residual 1.528 1.505 0.023 8.80e-03 1.29e+04 6.63e+00 bond pdb=" C ILE A 873 " pdb=" O ILE A 873 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.05e-02 9.07e+03 5.24e+00 bond pdb=" C LEU B 346 " pdb=" O LEU B 346 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.20e-02 6.94e+03 4.65e+00 bond pdb=" C ALA A 242 " pdb=" N ILE A 243 " ideal model delta sigma weight residual 1.333 1.308 0.025 1.20e-02 6.94e+03 4.41e+00 ... (remaining 12558 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.16: 226 104.16 - 111.64: 5702 111.64 - 119.11: 4450 119.11 - 126.59: 6430 126.59 - 134.06: 239 Bond angle restraints: 17047 Sorted by residual: angle pdb=" C ASP A 653 " pdb=" N PRO A 654 " pdb=" CA PRO A 654 " ideal model delta sigma weight residual 119.84 131.80 -11.96 1.25e+00 6.40e-01 9.15e+01 angle pdb=" N PHE B 210 " pdb=" CA PHE B 210 " pdb=" C PHE B 210 " ideal model delta sigma weight residual 108.45 115.91 -7.46 1.26e+00 6.30e-01 3.50e+01 angle pdb=" C PRO A 272 " pdb=" N LYS A 273 " pdb=" CA LYS A 273 " ideal model delta sigma weight residual 120.58 128.05 -7.47 1.32e+00 5.74e-01 3.20e+01 angle pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" O PHE B 151 " ideal model delta sigma weight residual 120.51 113.17 7.34 1.43e+00 4.89e-01 2.64e+01 angle pdb=" C LEU A 201 " pdb=" CA LEU A 201 " pdb=" CB LEU A 201 " ideal model delta sigma weight residual 116.63 111.05 5.58 1.16e+00 7.43e-01 2.31e+01 ... (remaining 17042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.79: 7030 14.79 - 29.58: 376 29.58 - 44.37: 57 44.37 - 59.16: 8 59.16 - 73.95: 7 Dihedral angle restraints: 7478 sinusoidal: 3016 harmonic: 4462 Sorted by residual: dihedral pdb=" C ASP A 333 " pdb=" N ASP A 333 " pdb=" CA ASP A 333 " pdb=" CB ASP A 333 " ideal model delta harmonic sigma weight residual -122.60 -137.32 14.72 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" CA GLY A 211 " pdb=" C GLY A 211 " pdb=" N TYR A 212 " pdb=" CA TYR A 212 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASN B 289 " pdb=" C ASN B 289 " pdb=" N THR B 290 " pdb=" CA THR B 290 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 7475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1771 0.112 - 0.225: 130 0.225 - 0.337: 2 0.337 - 0.450: 0 0.450 - 0.562: 1 Chirality restraints: 1904 Sorted by residual: chirality pdb=" CA ASP A 333 " pdb=" N ASP A 333 " pdb=" C ASP A 333 " pdb=" CB ASP A 333 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.89e+00 chirality pdb=" CA LEU A 200 " pdb=" N LEU A 200 " pdb=" C LEU A 200 " pdb=" CB LEU A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE A 243 " pdb=" CA ILE A 243 " pdb=" CG1 ILE A 243 " pdb=" CG2 ILE A 243 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1901 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1312 " 0.043 2.00e-02 2.50e+03 2.39e-02 1.42e+01 pdb=" CG TRP A1312 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A1312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A1312 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1312 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A1312 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A1312 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1312 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1312 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1312 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 653 " 0.060 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 654 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 654 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 654 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1074 " 0.016 2.00e-02 2.50e+03 2.38e-02 9.93e+00 pdb=" CG PHE A1074 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A1074 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A1074 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A1074 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A1074 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1074 " 0.004 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1710 2.76 - 3.29: 10398 3.29 - 3.83: 19956 3.83 - 4.36: 23703 4.36 - 4.90: 42357 Nonbonded interactions: 98124 Sorted by model distance: nonbonded pdb=" OG SER A 331 " pdb=" N TYR A 332 " model vdw 2.220 2.520 nonbonded pdb=" OG SER A 17 " pdb=" OG SER A 373 " model vdw 2.277 2.440 nonbonded pdb=" OG SER B 221 " pdb=" OD1 ASP B 223 " model vdw 2.279 2.440 nonbonded pdb=" O GLY A 276 " pdb=" OH TYR A 288 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR A 583 " pdb=" O GLY A 604 " model vdw 2.309 2.440 ... (remaining 98119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 2.230 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 36.250 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 12563 Z= 0.550 Angle : 1.040 12.185 17047 Z= 0.582 Chirality : 0.061 0.562 1904 Planarity : 0.008 0.089 2172 Dihedral : 9.963 73.946 4594 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.66 % Favored : 91.27 % Rotamer: Outliers : 0.89 % Allowed : 1.49 % Favored : 97.62 % Cbeta Deviations : 0.07 % 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: -4.00 (0.18), residues: 1512 helix: -4.44 (0.26), residues: 80 sheet: -2.21 (0.19), residues: 603 loop : -2.84 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A1312 HIS 0.012 0.003 HIS A 9 PHE 0.051 0.005 PHE A1074 TYR 0.040 0.004 TYR A 2 ARG 0.010 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 343 time to evaluate : 1.426 Fit side-chains REVERT: A 320 ILE cc_start: 0.7879 (pp) cc_final: 0.7512 (pt) REVERT: A 1208 THR cc_start: 0.7905 (t) cc_final: 0.7654 (p) REVERT: B 176 MET cc_start: 0.8663 (ttp) cc_final: 0.8387 (ttm) outliers start: 12 outliers final: 7 residues processed: 353 average time/residue: 0.3066 time to fit residues: 146.3444 Evaluate side-chains 166 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 346 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 25 ASN A 29 ASN A 85 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS ** A 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1089 ASN A1095 GLN B 69 ASN B 325 GLN B 343 HIS B 405 ASN B 416 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12563 Z= 0.195 Angle : 0.635 8.886 17047 Z= 0.333 Chirality : 0.046 0.217 1904 Planarity : 0.005 0.096 2172 Dihedral : 6.620 57.276 1682 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 2.16 % Allowed : 8.18 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.19), residues: 1512 helix: -3.23 (0.42), residues: 79 sheet: -1.61 (0.19), residues: 613 loop : -2.52 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1337 HIS 0.004 0.001 HIS B 287 PHE 0.022 0.002 PHE B 210 TYR 0.016 0.001 TYR A 2 ARG 0.006 0.001 ARG A1274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 1.477 Fit side-chains REVERT: A 320 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7558 (pt) REVERT: A 681 ARG cc_start: 0.7056 (ptm-80) cc_final: 0.6565 (ttm-80) REVERT: A 1208 THR cc_start: 0.7914 (t) cc_final: 0.7586 (p) outliers start: 29 outliers final: 14 residues processed: 217 average time/residue: 0.2387 time to fit residues: 75.4575 Evaluate side-chains 179 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 0.2980 chunk 115 optimal weight: 0.4980 chunk 94 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS A1393 ASN B 60 ASN B 310 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 12563 Z= 0.162 Angle : 0.569 8.149 17047 Z= 0.295 Chirality : 0.045 0.223 1904 Planarity : 0.005 0.098 2172 Dihedral : 5.666 41.746 1674 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 2.60 % Allowed : 10.33 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1512 helix: -2.07 (0.51), residues: 80 sheet: -1.20 (0.19), residues: 634 loop : -2.25 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1337 HIS 0.004 0.001 HIS A1372 PHE 0.012 0.001 PHE B 210 TYR 0.013 0.001 TYR A 2 ARG 0.004 0.000 ARG A 857 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 256 TRP cc_start: 0.7839 (t60) cc_final: 0.7460 (t60) REVERT: A 1208 THR cc_start: 0.7782 (t) cc_final: 0.7468 (p) REVERT: A 1273 ASP cc_start: 0.8005 (p0) cc_final: 0.7743 (p0) outliers start: 35 outliers final: 20 residues processed: 216 average time/residue: 0.2321 time to fit residues: 74.1993 Evaluate side-chains 183 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1176 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12563 Z= 0.423 Angle : 0.701 9.126 17047 Z= 0.360 Chirality : 0.049 0.226 1904 Planarity : 0.005 0.101 2172 Dihedral : 5.953 39.735 1674 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.20 % Favored : 91.73 % Rotamer: Outliers : 3.64 % Allowed : 11.82 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.20), residues: 1512 helix: -1.52 (0.57), residues: 79 sheet: -1.10 (0.20), residues: 623 loop : -2.15 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1312 HIS 0.007 0.002 HIS A 9 PHE 0.021 0.003 PHE A 892 TYR 0.022 0.002 TYR A 345 ARG 0.005 0.001 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 155 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 392 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8614 (pp) REVERT: A 659 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7415 (ttm) outliers start: 49 outliers final: 33 residues processed: 188 average time/residue: 0.2029 time to fit residues: 59.3898 Evaluate side-chains 180 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 145 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 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 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN A 636 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12563 Z= 0.174 Angle : 0.569 6.609 17047 Z= 0.294 Chirality : 0.045 0.234 1904 Planarity : 0.004 0.106 2172 Dihedral : 5.505 42.683 1673 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.58 % Rotamer: Outliers : 2.45 % Allowed : 13.68 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1512 helix: -1.00 (0.60), residues: 79 sheet: -0.90 (0.20), residues: 633 loop : -2.01 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1337 HIS 0.005 0.001 HIS A1372 PHE 0.011 0.001 PHE B 198 TYR 0.013 0.001 TYR A 19 ARG 0.004 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 256 TRP cc_start: 0.7843 (t60) cc_final: 0.7478 (t60) REVERT: A 1092 ILE cc_start: 0.8783 (mm) cc_final: 0.8553 (mm) REVERT: A 1336 THR cc_start: 0.7279 (p) cc_final: 0.7041 (p) outliers start: 33 outliers final: 25 residues processed: 184 average time/residue: 0.2140 time to fit residues: 60.9076 Evaluate side-chains 179 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 0.0470 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 overall best weight: 2.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1393 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12563 Z= 0.318 Angle : 0.633 7.598 17047 Z= 0.325 Chirality : 0.047 0.244 1904 Planarity : 0.005 0.108 2172 Dihedral : 5.657 47.760 1673 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.94 % Favored : 92.00 % Rotamer: Outliers : 3.35 % Allowed : 13.38 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.21), residues: 1512 helix: -0.73 (0.62), residues: 79 sheet: -0.81 (0.20), residues: 616 loop : -1.91 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1312 HIS 0.006 0.001 HIS A 9 PHE 0.018 0.002 PHE A 892 TYR 0.023 0.002 TYR A 989 ARG 0.004 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 1092 ILE cc_start: 0.8784 (mm) cc_final: 0.8554 (mm) REVERT: A 1273 ASP cc_start: 0.8022 (p0) cc_final: 0.7753 (p0) REVERT: A 1400 ASP cc_start: 0.8100 (t0) cc_final: 0.7887 (t0) REVERT: B 210 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.5905 (p90) outliers start: 45 outliers final: 32 residues processed: 186 average time/residue: 0.2102 time to fit residues: 60.2008 Evaluate side-chains 184 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12563 Z= 0.210 Angle : 0.572 6.756 17047 Z= 0.294 Chirality : 0.045 0.235 1904 Planarity : 0.004 0.109 2172 Dihedral : 5.504 54.968 1673 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.42 % Favored : 93.52 % Rotamer: Outliers : 2.75 % Allowed : 13.83 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.21), residues: 1512 helix: -0.40 (0.63), residues: 79 sheet: -0.68 (0.20), residues: 621 loop : -1.84 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1337 HIS 0.004 0.001 HIS A1372 PHE 0.012 0.001 PHE B 198 TYR 0.020 0.001 TYR A 989 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: B 75 ASP cc_start: 0.6828 (m-30) cc_final: 0.6554 (m-30) outliers start: 37 outliers final: 32 residues processed: 183 average time/residue: 0.2115 time to fit residues: 59.7919 Evaluate side-chains 180 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1128 MET Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 141 optimal weight: 0.7980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12563 Z= 0.285 Angle : 0.609 7.638 17047 Z= 0.311 Chirality : 0.046 0.230 1904 Planarity : 0.005 0.110 2172 Dihedral : 5.531 52.714 1673 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.74 % Favored : 92.20 % Rotamer: Outliers : 2.97 % Allowed : 14.05 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1512 helix: -0.34 (0.62), residues: 79 sheet: -0.66 (0.20), residues: 622 loop : -1.76 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1312 HIS 0.005 0.001 HIS A 9 PHE 0.015 0.002 PHE B 198 TYR 0.022 0.001 TYR A 989 ARG 0.003 0.000 ARG A1298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 1400 ASP cc_start: 0.8099 (t0) cc_final: 0.7874 (t0) REVERT: B 75 ASP cc_start: 0.6781 (m-30) cc_final: 0.6461 (m-30) outliers start: 40 outliers final: 36 residues processed: 176 average time/residue: 0.2044 time to fit residues: 55.8876 Evaluate side-chains 183 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 147 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12563 Z= 0.198 Angle : 0.574 7.099 17047 Z= 0.294 Chirality : 0.045 0.232 1904 Planarity : 0.004 0.112 2172 Dihedral : 5.247 35.736 1673 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 2.60 % Allowed : 14.57 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1512 helix: -0.15 (0.63), residues: 79 sheet: -0.50 (0.21), residues: 612 loop : -1.71 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1337 HIS 0.004 0.001 HIS A1372 PHE 0.016 0.001 PHE B 198 TYR 0.022 0.001 TYR A 989 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: A 1273 ASP cc_start: 0.7894 (p0) cc_final: 0.7672 (p0) REVERT: B 75 ASP cc_start: 0.6682 (m-30) cc_final: 0.6412 (m-30) REVERT: B 213 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7602 (t) outliers start: 35 outliers final: 29 residues processed: 174 average time/residue: 0.2202 time to fit residues: 60.2409 Evaluate side-chains 176 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1128 MET Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 121 optimal weight: 0.3980 chunk 12 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12563 Z= 0.393 Angle : 0.677 9.397 17047 Z= 0.344 Chirality : 0.048 0.247 1904 Planarity : 0.005 0.114 2172 Dihedral : 5.521 34.027 1671 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 2.83 % Allowed : 14.28 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.21), residues: 1512 helix: -0.30 (0.62), residues: 79 sheet: -0.64 (0.21), residues: 625 loop : -1.68 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1312 HIS 0.007 0.001 HIS A 9 PHE 0.020 0.002 PHE A 892 TYR 0.025 0.002 TYR A 989 ARG 0.004 0.001 ARG A1313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 1.457 Fit side-chains REVERT: A 592 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6689 (tt) REVERT: A 1273 ASP cc_start: 0.7986 (p0) cc_final: 0.7646 (p0) REVERT: A 1400 ASP cc_start: 0.8128 (t0) cc_final: 0.7888 (t0) outliers start: 38 outliers final: 33 residues processed: 166 average time/residue: 0.2208 time to fit residues: 57.4339 Evaluate side-chains 168 residues out of total 1345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 693 SER Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 999 SER Chi-restraints excluded: chain A residue 1039 SER Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1312 TRP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1412 THR Chi-restraints excluded: chain A residue 1442 HIS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105795 restraints weight = 17497.238| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.16 r_work: 0.3101 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12563 Z= 0.202 Angle : 0.585 9.122 17047 Z= 0.298 Chirality : 0.046 0.242 1904 Planarity : 0.005 0.115 2172 Dihedral : 5.170 35.788 1669 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 2.45 % Allowed : 14.72 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1512 helix: -0.20 (0.63), residues: 79 sheet: -0.41 (0.21), residues: 604 loop : -1.71 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1337 HIS 0.005 0.001 HIS A 636 PHE 0.017 0.001 PHE B 198 TYR 0.023 0.001 TYR A 989 ARG 0.003 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2687.29 seconds wall clock time: 49 minutes 54.22 seconds (2994.22 seconds total)