Starting phenix.real_space_refine on Wed Feb 14 16:30:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/02_2024/6msm_9230_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/02_2024/6msm_9230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/02_2024/6msm_9230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/02_2024/6msm_9230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/02_2024/6msm_9230_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/02_2024/6msm_9230_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.056 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6343 2.51 5 N 1596 2.21 5 O 1709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 933": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1158": "NH1" <-> "NH2" Residue "A ARG 1239": "NH1" <-> "NH2" Residue "A ARG 1259": "NH1" <-> "NH2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A ARG 1325": "NH1" <-> "NH2" Residue "A ARG 1358": "NH1" <-> "NH2" Residue "A ARG 1386": "NH1" <-> "NH2" 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: 9703 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1181, 9466 Classifications: {'peptide': 1181} Link IDs: {'PTRANS': 32, 'TRANS': 1148} Chain breaks: 4 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 175 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: 55 Time building chain proxies: 5.85, per 1000 atoms: 0.60 Number of scatterers: 9703 At special positions: 0 Unit cell: (81.37, 88.58, 144.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1709 8.00 N 1596 7.00 C 6343 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: 3.94 Conformation dependent library (CDL) restraints added in 1.7 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 5 sheets defined 61.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.997A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.873A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.542A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 165 removed outlier: 5.088A pdb=" N ILE A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.628A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 194 removed outlier: 3.547A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASN A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.689A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.773A pdb=" N GLY A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 215 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 217 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 245 removed outlier: 4.058A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 removed outlier: 4.148A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 279 through 308 removed outlier: 4.244A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 328 removed outlier: 3.715A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.706A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.916A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 375 removed outlier: 3.729A pdb=" N GLN A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 527 through 531 Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.688A pdb=" N LYS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 848 through 851 No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 857 through 885 Processing helix chain 'A' and resid 908 through 921 removed outlier: 4.040A pdb=" N SER A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 926 No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 934 through 958 Processing helix chain 'A' and resid 961 through 965 Processing helix chain 'A' and resid 969 through 984 removed outlier: 3.611A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE A 980 " --> pdb=" O PHE A 976 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1011 removed outlier: 3.620A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1060 removed outlier: 3.672A pdb=" N VAL A1020 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.980A pdb=" N VAL A1024 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A1028 " --> pdb=" O ALA A1025 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A1029 " --> pdb=" O PHE A1026 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A1034 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN A1035 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN A1038 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A1041 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A1042 " --> pdb=" O GLN A1039 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A1044 " --> pdb=" O LYS A1041 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A1045 " --> pdb=" O GLN A1042 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A1046 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.905A pdb=" N THR A1053 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A1054 " --> pdb=" O ILE A1051 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A1056 " --> pdb=" O THR A1053 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A1057 " --> pdb=" O HIS A1054 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A1058 " --> pdb=" O LEU A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1120 removed outlier: 3.958A pdb=" N ALA A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A1091 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A1099 " --> pdb=" O THR A1095 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1167 removed outlier: 3.995A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1136 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A1141 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.617A pdb=" N PHE A1257 " --> pdb=" O LEU A1253 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1283 Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1322 removed outlier: 3.562A pdb=" N ASP A1320 " --> pdb=" O TRP A1316 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 3.603A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1325 through 1329' Processing helix chain 'A' and resid 1348 through 1361 removed outlier: 3.568A pdb=" N GLN A1352 " --> pdb=" O HIS A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1390 removed outlier: 3.568A pdb=" N LYS A1389 " --> pdb=" O ARG A1386 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN A1390 " --> pdb=" O THR A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.533A pdb=" N LEU A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1433 removed outlier: 3.511A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 No H-bonds generated for 'chain 'A' and resid 1436 through 1439' Processing helix chain 'A' and resid 1443 through 1449 removed outlier: 4.139A pdb=" N LYS A1448 " --> pdb=" O SER A1444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A1449 " --> pdb=" O ASP A1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.756A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 481 through 483 removed outlier: 3.556A pdb=" N LYS A 483 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 393 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 454 through 457 removed outlier: 7.062A pdb=" N LYS A 615 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA A 457 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 617 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.568A pdb=" N LEU A 568 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N CYS A 491 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 570 " --> pdb=" O CYS A 491 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1232 through 1234 removed outlier: 3.588A pdb=" N MET A1210 " --> pdb=" O ILE A1234 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1420 through 1424 removed outlier: 3.680A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLY A1244 " --> pdb=" O LEU A1399 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 4.28 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: 2875 1.34 - 1.46: 1310 1.46 - 1.58: 5629 1.58 - 1.70: 10 1.70 - 1.82: 79 Bond restraints: 9903 Sorted by residual: bond pdb=" N LEU A 935 " pdb=" CA LEU A 935 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.22e+01 bond pdb=" N ILE A1277 " pdb=" CA ILE A1277 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N VAL A 350 " pdb=" CA VAL A 350 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.09e-02 8.42e+03 1.13e+01 bond pdb=" N VAL A1318 " pdb=" CA VAL A1318 " ideal model delta sigma weight residual 1.460 1.500 -0.041 1.21e-02 6.83e+03 1.13e+01 bond pdb=" C5 ATP A1504 " pdb=" C6 ATP A1504 " ideal model delta sigma weight residual 1.409 1.442 -0.033 1.00e-02 1.00e+04 1.11e+01 ... (remaining 9898 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.48: 229 106.48 - 113.50: 5362 113.50 - 120.53: 4341 120.53 - 127.55: 3386 127.55 - 134.58: 72 Bond angle restraints: 13390 Sorted by residual: angle pdb=" PB ATP A1504 " pdb=" O3B ATP A1504 " pdb=" PG ATP A1504 " ideal model delta sigma weight residual 139.87 122.97 16.90 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PA ATP A1504 " pdb=" O3A ATP A1504 " pdb=" PB ATP A1504 " ideal model delta sigma weight residual 136.83 121.68 15.15 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 125.08 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" PA ATP A1503 " pdb=" O3A ATP A1503 " pdb=" PB ATP A1503 " ideal model delta sigma weight residual 136.83 123.00 13.83 1.00e+00 1.00e+00 1.91e+02 angle pdb=" C THR A 390 " pdb=" CA THR A 390 " pdb=" CB THR A 390 " ideal model delta sigma weight residual 111.86 123.12 -11.26 1.34e+00 5.57e-01 7.06e+01 ... (remaining 13385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 5521 19.02 - 38.03: 348 38.03 - 57.05: 95 57.05 - 76.06: 11 76.06 - 95.08: 4 Dihedral angle restraints: 5979 sinusoidal: 2497 harmonic: 3482 Sorted by residual: dihedral pdb=" CA ASN A 187 " pdb=" C ASN A 187 " pdb=" N LEU A 188 " pdb=" CA LEU A 188 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL A1288 " pdb=" C VAL A1288 " pdb=" N ILE A1289 " pdb=" CA ILE A1289 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C THR A 390 " pdb=" N THR A 390 " pdb=" CA THR A 390 " pdb=" CB THR A 390 " ideal model delta harmonic sigma weight residual -122.00 -132.90 10.90 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 5976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 583 0.042 - 0.084: 464 0.084 - 0.127: 346 0.127 - 0.169: 132 0.169 - 0.211: 20 Chirality restraints: 1545 Sorted by residual: 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 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA VAL A 855 " pdb=" N VAL A 855 " pdb=" C VAL A 855 " pdb=" CB VAL A 855 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA THR A 351 " pdb=" N THR A 351 " pdb=" C THR A 351 " pdb=" CB THR A 351 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1542 not shown) Planarity restraints: 1628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1126 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C GLU A1126 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU A1126 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A1127 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 390 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C THR A 390 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 390 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 391 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 348 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C MET A 348 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 348 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 349 " 0.013 2.00e-02 2.50e+03 ... (remaining 1625 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 26 2.54 - 3.13: 6969 3.13 - 3.72: 14413 3.72 - 4.31: 20292 4.31 - 4.90: 34248 Nonbonded interactions: 75948 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.955 2.170 nonbonded pdb=" O ASP A 112 " pdb=" OD1 ASP A 112 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.053 2.170 nonbonded pdb="MG MG A1501 " pdb=" O2B ATP A1503 " model vdw 2.142 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.187 2.170 ... (remaining 75943 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: 1.630 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: 5.990 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.470 Find NCS groups from input model: 0.250 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 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 : 0.012 0.044 9903 Z= 0.762 Angle : 1.511 16.903 13390 Z= 1.118 Chirality : 0.078 0.211 1545 Planarity : 0.005 0.058 1628 Dihedral : 13.911 95.076 3727 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.39 % Allowed : 5.11 % Favored : 94.50 % Cbeta Deviations : 0.09 % 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: -2.75 (0.20), residues: 1171 helix: -1.39 (0.16), residues: 732 sheet: -1.94 (0.61), residues: 69 loop : -2.39 (0.25), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1274 HIS 0.008 0.002 HIS A 146 PHE 0.014 0.003 PHE A 337 TYR 0.031 0.003 TYR A 161 ARG 0.011 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 267 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8416 (mptt) cc_final: 0.7940 (tppt) REVERT: A 15 LEU cc_start: 0.8680 (tp) cc_final: 0.8404 (tt) REVERT: A 26 LYS cc_start: 0.8242 (tptp) cc_final: 0.7999 (tttp) REVERT: A 31 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7446 (ttt90) REVERT: A 51 GLU cc_start: 0.8301 (tp30) cc_final: 0.8092 (tp30) REVERT: A 68 LYS cc_start: 0.8211 (mttt) cc_final: 0.7939 (mtpp) REVERT: A 129 LEU cc_start: 0.8313 (tt) cc_final: 0.8099 (mm) REVERT: A 224 PHE cc_start: 0.7534 (m-80) cc_final: 0.6940 (t80) REVERT: A 235 LEU cc_start: 0.8815 (mt) cc_final: 0.8537 (mm) REVERT: A 246 LYS cc_start: 0.8030 (ttpp) cc_final: 0.7745 (tmtt) REVERT: A 315 PHE cc_start: 0.8192 (t80) cc_final: 0.7713 (t80) REVERT: A 351 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8057 (t) REVERT: A 362 TYR cc_start: 0.8183 (m-80) cc_final: 0.7983 (m-80) REVERT: A 373 ASP cc_start: 0.8027 (t70) cc_final: 0.7817 (t0) REVERT: A 383 LEU cc_start: 0.7771 (tt) cc_final: 0.7087 (tt) REVERT: A 448 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7910 (mm) REVERT: A 476 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8998 (pm20) REVERT: A 504 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7952 (mt-10) REVERT: A 532 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8448 (ttmt) REVERT: A 905 VAL cc_start: 0.8528 (t) cc_final: 0.8238 (p) REVERT: A 958 GLN cc_start: 0.7794 (pt0) cc_final: 0.7581 (pt0) REVERT: A 985 ASP cc_start: 0.8299 (m-30) cc_final: 0.8063 (m-30) REVERT: A 1046 GLU cc_start: 0.7994 (tt0) cc_final: 0.7502 (tp30) REVERT: A 1060 LYS cc_start: 0.8190 (tttt) cc_final: 0.7850 (ttpt) REVERT: A 1137 MET cc_start: 0.8567 (mmm) cc_final: 0.8280 (mmp) REVERT: A 1224 ASN cc_start: 0.7629 (m110) cc_final: 0.7201 (t0) REVERT: A 1330 GLN cc_start: 0.8461 (tt0) cc_final: 0.8138 (mt0) REVERT: A 1341 ASP cc_start: 0.8253 (t0) cc_final: 0.7949 (t0) REVERT: A 1416 ILE cc_start: 0.8511 (mt) cc_final: 0.8161 (tt) REVERT: A 1444 SER cc_start: 0.7816 (m) cc_final: 0.7304 (t) outliers start: 4 outliers final: 0 residues processed: 270 average time/residue: 0.2712 time to fit residues: 96.3866 Evaluate side-chains 148 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN ** A 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A1088 ASN ** A1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9903 Z= 0.207 Angle : 0.586 6.799 13390 Z= 0.306 Chirality : 0.041 0.209 1545 Planarity : 0.004 0.038 1628 Dihedral : 9.234 82.422 1470 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.83 % Allowed : 11.96 % Favored : 86.21 % 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: -0.64 (0.22), residues: 1171 helix: 0.36 (0.18), residues: 735 sheet: -1.46 (0.59), residues: 69 loop : -1.69 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 202 HIS 0.005 0.001 HIS A 199 PHE 0.026 0.001 PHE A 236 TYR 0.015 0.001 TYR A 517 ARG 0.006 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.129 Fit side-chains REVERT: A 8 LYS cc_start: 0.8495 (mptt) cc_final: 0.8067 (tppt) REVERT: A 31 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7356 (ttm170) REVERT: A 51 GLU cc_start: 0.8332 (tp30) cc_final: 0.8055 (tp30) REVERT: A 64 LYS cc_start: 0.6737 (mmtt) cc_final: 0.6209 (mmtp) REVERT: A 68 LYS cc_start: 0.8341 (mttt) cc_final: 0.8100 (mtpp) REVERT: A 315 PHE cc_start: 0.7858 (t80) cc_final: 0.7614 (t80) REVERT: A 362 TYR cc_start: 0.8043 (m-80) cc_final: 0.7797 (m-80) REVERT: A 391 GLU cc_start: 0.8111 (tt0) cc_final: 0.7509 (tm-30) REVERT: A 469 MET cc_start: 0.7669 (mmm) cc_final: 0.7468 (mmp) REVERT: A 504 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 532 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8248 (tppt) REVERT: A 636 LEU cc_start: 0.9173 (tt) cc_final: 0.8906 (mt) REVERT: A 1224 ASN cc_start: 0.7587 (m110) cc_final: 0.7022 (t0) REVERT: A 1228 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8036 (mt-10) REVERT: A 1280 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7920 (tm-30) REVERT: A 1341 ASP cc_start: 0.8072 (t0) cc_final: 0.7746 (t0) outliers start: 19 outliers final: 12 residues processed: 193 average time/residue: 0.2053 time to fit residues: 56.9059 Evaluate side-chains 146 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1404 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS A1100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9903 Z= 0.187 Angle : 0.540 8.248 13390 Z= 0.274 Chirality : 0.039 0.181 1545 Planarity : 0.003 0.035 1628 Dihedral : 7.930 85.757 1467 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.51 % Allowed : 14.46 % Favored : 83.03 % 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: 0.03 (0.24), residues: 1171 helix: 0.88 (0.19), residues: 741 sheet: -1.52 (0.57), residues: 71 loop : -1.36 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 202 HIS 0.004 0.001 HIS A1085 PHE 0.024 0.001 PHE A 626 TYR 0.013 0.001 TYR A 919 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8480 (mptt) cc_final: 0.8026 (tppt) REVERT: A 31 ARG cc_start: 0.7621 (ttm170) cc_final: 0.7245 (ttm170) REVERT: A 51 GLU cc_start: 0.8355 (tp30) cc_final: 0.8107 (tp30) REVERT: A 64 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6346 (mmtp) REVERT: A 68 LYS cc_start: 0.8363 (mttt) cc_final: 0.8142 (mtpp) REVERT: A 78 PHE cc_start: 0.8096 (t80) cc_final: 0.7486 (t80) REVERT: A 362 TYR cc_start: 0.8026 (m-80) cc_final: 0.7779 (m-80) REVERT: A 391 GLU cc_start: 0.8127 (tt0) cc_final: 0.7803 (tt0) REVERT: A 504 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 532 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8129 (tppt) REVERT: A 636 LEU cc_start: 0.9162 (tt) cc_final: 0.8833 (pp) REVERT: A 1224 ASN cc_start: 0.7534 (m110) cc_final: 0.6942 (t0) REVERT: A 1280 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7932 (tm-30) REVERT: A 1341 ASP cc_start: 0.7994 (t0) cc_final: 0.7680 (t0) outliers start: 26 outliers final: 18 residues processed: 176 average time/residue: 0.2079 time to fit residues: 52.8422 Evaluate side-chains 155 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1111 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9903 Z= 0.214 Angle : 0.534 7.063 13390 Z= 0.272 Chirality : 0.040 0.180 1545 Planarity : 0.003 0.031 1628 Dihedral : 7.039 79.303 1467 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.99 % Allowed : 14.75 % Favored : 82.26 % 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: 0.30 (0.24), residues: 1171 helix: 1.04 (0.19), residues: 744 sheet: -1.28 (0.56), residues: 76 loop : -1.18 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 216 HIS 0.005 0.001 HIS A1085 PHE 0.019 0.001 PHE A 236 TYR 0.011 0.001 TYR A 517 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8651 (mptt) cc_final: 0.8165 (tppt) REVERT: A 31 ARG cc_start: 0.7681 (ttm170) cc_final: 0.7290 (ttm170) REVERT: A 51 GLU cc_start: 0.8396 (tp30) cc_final: 0.8180 (tp30) REVERT: A 64 LYS cc_start: 0.6619 (mmtt) cc_final: 0.6072 (mmtp) REVERT: A 68 LYS cc_start: 0.8409 (mttt) cc_final: 0.8202 (mtpp) REVERT: A 78 PHE cc_start: 0.8109 (t80) cc_final: 0.7471 (t80) REVERT: A 362 TYR cc_start: 0.8057 (m-80) cc_final: 0.7815 (m-80) REVERT: A 504 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 532 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8164 (tppt) REVERT: A 1224 ASN cc_start: 0.7481 (m110) cc_final: 0.6849 (t0) REVERT: A 1280 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 1341 ASP cc_start: 0.7923 (t0) cc_final: 0.7633 (t0) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.2074 time to fit residues: 49.3846 Evaluate side-chains 145 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1322 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9903 Z= 0.176 Angle : 0.509 6.955 13390 Z= 0.257 Chirality : 0.038 0.174 1545 Planarity : 0.003 0.029 1628 Dihedral : 6.488 73.179 1467 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.09 % Allowed : 15.53 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1171 helix: 1.18 (0.19), residues: 743 sheet: -1.02 (0.56), residues: 75 loop : -1.04 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.005 0.001 HIS A 939 PHE 0.025 0.001 PHE A 236 TYR 0.012 0.001 TYR A 517 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.152 Fit side-chains REVERT: A 8 LYS cc_start: 0.8634 (mptt) cc_final: 0.8162 (tppt) REVERT: A 31 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7340 (ttm170) REVERT: A 51 GLU cc_start: 0.8343 (tp30) cc_final: 0.8122 (tm-30) REVERT: A 64 LYS cc_start: 0.6523 (mmtt) cc_final: 0.6035 (mmtp) REVERT: A 78 PHE cc_start: 0.8119 (t80) cc_final: 0.7360 (t80) REVERT: A 249 ASP cc_start: 0.8540 (m-30) cc_final: 0.8125 (p0) REVERT: A 469 MET cc_start: 0.7699 (mmp) cc_final: 0.7318 (mmp) REVERT: A 504 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 532 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8146 (tppt) REVERT: A 636 LEU cc_start: 0.9264 (tt) cc_final: 0.8976 (mt) REVERT: A 1280 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 1330 GLN cc_start: 0.8479 (mt0) cc_final: 0.8163 (mt0) REVERT: A 1341 ASP cc_start: 0.7878 (t0) cc_final: 0.7582 (t0) outliers start: 32 outliers final: 24 residues processed: 161 average time/residue: 0.2064 time to fit residues: 47.5669 Evaluate side-chains 146 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1410 CYS Chi-restraints excluded: chain A residue 1416 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9903 Z= 0.232 Angle : 0.540 7.193 13390 Z= 0.271 Chirality : 0.039 0.169 1545 Planarity : 0.003 0.029 1628 Dihedral : 6.420 66.284 1467 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.66 % Allowed : 16.20 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1171 helix: 1.13 (0.19), residues: 746 sheet: -1.02 (0.55), residues: 75 loop : -0.94 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1145 HIS 0.005 0.001 HIS A1085 PHE 0.021 0.001 PHE A 236 TYR 0.011 0.001 TYR A1381 ARG 0.005 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.040 Fit side-chains REVERT: A 8 LYS cc_start: 0.8677 (mptt) cc_final: 0.8226 (tppt) REVERT: A 31 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7381 (ttm170) REVERT: A 51 GLU cc_start: 0.8345 (tp30) cc_final: 0.8112 (tm-30) REVERT: A 64 LYS cc_start: 0.6419 (mmtt) cc_final: 0.5924 (mmtp) REVERT: A 249 ASP cc_start: 0.8628 (m-30) cc_final: 0.8170 (p0) REVERT: A 504 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7813 (mt-10) REVERT: A 532 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8166 (tppt) REVERT: A 626 PHE cc_start: 0.7478 (t80) cc_final: 0.7128 (t80) REVERT: A 636 LEU cc_start: 0.9263 (tt) cc_final: 0.8936 (pp) REVERT: A 1280 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 1330 GLN cc_start: 0.8478 (mt0) cc_final: 0.8150 (mt0) REVERT: A 1341 ASP cc_start: 0.7926 (t0) cc_final: 0.7638 (t0) outliers start: 38 outliers final: 29 residues processed: 159 average time/residue: 0.2016 time to fit residues: 47.7665 Evaluate side-chains 153 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 877 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1410 CYS Chi-restraints excluded: chain A residue 1416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9903 Z= 0.262 Angle : 0.552 7.196 13390 Z= 0.278 Chirality : 0.040 0.172 1545 Planarity : 0.003 0.029 1628 Dihedral : 6.466 57.930 1467 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.38 % Allowed : 16.97 % Favored : 79.65 % 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: 0.45 (0.25), residues: 1171 helix: 1.06 (0.19), residues: 748 sheet: -1.18 (0.54), residues: 76 loop : -0.88 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 865 HIS 0.005 0.001 HIS A1085 PHE 0.021 0.001 PHE A1111 TYR 0.011 0.001 TYR A1381 ARG 0.006 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 1.208 Fit side-chains REVERT: A 8 LYS cc_start: 0.8746 (mptt) cc_final: 0.8365 (tppt) REVERT: A 31 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7507 (ttt90) REVERT: A 51 GLU cc_start: 0.8259 (tp30) cc_final: 0.8042 (tm-30) REVERT: A 64 LYS cc_start: 0.6517 (mmtt) cc_final: 0.5994 (mmtp) REVERT: A 78 PHE cc_start: 0.8206 (t80) cc_final: 0.7666 (t80) REVERT: A 279 GLU cc_start: 0.7826 (mp0) cc_final: 0.7530 (mp0) REVERT: A 469 MET cc_start: 0.7835 (mmp) cc_final: 0.7395 (mmp) REVERT: A 472 MET cc_start: 0.8198 (mtm) cc_final: 0.7967 (mtm) REVERT: A 504 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 532 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8186 (tppt) REVERT: A 626 PHE cc_start: 0.7489 (t80) cc_final: 0.7118 (t80) REVERT: A 636 LEU cc_start: 0.9267 (tt) cc_final: 0.8946 (pp) REVERT: A 1111 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7667 (t80) REVERT: A 1280 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7981 (tm-30) REVERT: A 1330 GLN cc_start: 0.8494 (mt0) cc_final: 0.8135 (mt0) REVERT: A 1341 ASP cc_start: 0.7988 (t0) cc_final: 0.7709 (t0) outliers start: 35 outliers final: 30 residues processed: 157 average time/residue: 0.1982 time to fit residues: 45.9916 Evaluate side-chains 157 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1111 PHE Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1275 ASP Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1410 CYS Chi-restraints excluded: chain A residue 1416 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 56 optimal weight: 0.0030 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9903 Z= 0.148 Angle : 0.507 9.139 13390 Z= 0.252 Chirality : 0.038 0.165 1545 Planarity : 0.003 0.029 1628 Dihedral : 5.994 54.265 1467 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.31 % Allowed : 18.42 % Favored : 79.27 % 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: 0.71 (0.25), residues: 1171 helix: 1.28 (0.20), residues: 746 sheet: -0.95 (0.54), residues: 75 loop : -0.87 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 202 HIS 0.004 0.001 HIS A 199 PHE 0.018 0.001 PHE A 236 TYR 0.010 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 1.119 Fit side-chains REVERT: A 8 LYS cc_start: 0.8731 (mptt) cc_final: 0.8337 (tppt) REVERT: A 31 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7461 (ttm170) REVERT: A 64 LYS cc_start: 0.6415 (mmtt) cc_final: 0.5930 (mmtp) REVERT: A 78 PHE cc_start: 0.8129 (t80) cc_final: 0.7567 (t80) REVERT: A 249 ASP cc_start: 0.8519 (m-30) cc_final: 0.8130 (p0) REVERT: A 279 GLU cc_start: 0.7802 (mp0) cc_final: 0.7484 (mp0) REVERT: A 450 ARG cc_start: 0.7529 (ptt90) cc_final: 0.7121 (ptm160) REVERT: A 469 MET cc_start: 0.7688 (mmp) cc_final: 0.7271 (mmp) REVERT: A 476 GLU cc_start: 0.9119 (mp0) cc_final: 0.8828 (pm20) REVERT: A 504 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7833 (mt-10) REVERT: A 532 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8159 (tppt) REVERT: A 626 PHE cc_start: 0.7369 (t80) cc_final: 0.7038 (t80) REVERT: A 636 LEU cc_start: 0.9284 (tt) cc_final: 0.8990 (pp) REVERT: A 1166 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7298 (t80) REVERT: A 1280 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 1330 GLN cc_start: 0.8478 (mt0) cc_final: 0.8112 (mt0) REVERT: A 1341 ASP cc_start: 0.7828 (t0) cc_final: 0.7536 (t0) outliers start: 24 outliers final: 19 residues processed: 171 average time/residue: 0.2042 time to fit residues: 51.2176 Evaluate side-chains 156 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0570 chunk 109 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9903 Z= 0.143 Angle : 0.516 8.710 13390 Z= 0.254 Chirality : 0.038 0.161 1545 Planarity : 0.003 0.030 1628 Dihedral : 5.700 59.782 1467 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.60 % Allowed : 19.00 % Favored : 78.40 % 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: 0.84 (0.25), residues: 1171 helix: 1.37 (0.20), residues: 741 sheet: -0.76 (0.53), residues: 76 loop : -0.79 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 202 HIS 0.004 0.001 HIS A 199 PHE 0.023 0.001 PHE A 236 TYR 0.009 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.094 Fit side-chains REVERT: A 8 LYS cc_start: 0.8715 (mptt) cc_final: 0.8333 (tppt) REVERT: A 31 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7417 (ttm170) REVERT: A 64 LYS cc_start: 0.6275 (mmtt) cc_final: 0.5837 (mmtp) REVERT: A 78 PHE cc_start: 0.8104 (t80) cc_final: 0.7569 (t80) REVERT: A 249 ASP cc_start: 0.8456 (m-30) cc_final: 0.8062 (p0) REVERT: A 450 ARG cc_start: 0.7591 (ptt90) cc_final: 0.7136 (ptm160) REVERT: A 504 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 532 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8129 (tppt) REVERT: A 626 PHE cc_start: 0.7384 (t80) cc_final: 0.7048 (t80) REVERT: A 636 LEU cc_start: 0.9280 (tt) cc_final: 0.8990 (pp) REVERT: A 1128 ARG cc_start: 0.6720 (tpt170) cc_final: 0.6251 (mtm180) REVERT: A 1166 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7281 (t80) REVERT: A 1169 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8132 (mtm) REVERT: A 1280 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 1330 GLN cc_start: 0.8467 (mt0) cc_final: 0.8116 (mt0) REVERT: A 1341 ASP cc_start: 0.7836 (t0) cc_final: 0.7544 (t0) outliers start: 27 outliers final: 23 residues processed: 163 average time/residue: 0.2070 time to fit residues: 48.5460 Evaluate side-chains 157 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9903 Z= 0.218 Angle : 0.542 9.174 13390 Z= 0.269 Chirality : 0.039 0.169 1545 Planarity : 0.003 0.029 1628 Dihedral : 5.761 55.840 1467 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.51 % Allowed : 19.67 % Favored : 77.82 % 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: 0.71 (0.25), residues: 1171 helix: 1.25 (0.20), residues: 741 sheet: -0.99 (0.53), residues: 75 loop : -0.75 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1089 HIS 0.005 0.001 HIS A1085 PHE 0.023 0.001 PHE A 236 TYR 0.011 0.001 TYR A1381 ARG 0.004 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.035 Fit side-chains REVERT: A 8 LYS cc_start: 0.8746 (mptt) cc_final: 0.8428 (tppt) REVERT: A 31 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7335 (ttt90) REVERT: A 64 LYS cc_start: 0.6473 (mmtt) cc_final: 0.5956 (mmtp) REVERT: A 78 PHE cc_start: 0.8191 (t80) cc_final: 0.7636 (t80) REVERT: A 102 LEU cc_start: 0.7577 (tp) cc_final: 0.7169 (mp) REVERT: A 450 ARG cc_start: 0.7531 (ptt90) cc_final: 0.7114 (ptm160) REVERT: A 469 MET cc_start: 0.7615 (mmm) cc_final: 0.7129 (mmp) REVERT: A 476 GLU cc_start: 0.9207 (mp0) cc_final: 0.8957 (pm20) REVERT: A 504 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7795 (mt-10) REVERT: A 532 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8154 (tppt) REVERT: A 626 PHE cc_start: 0.7411 (t80) cc_final: 0.7057 (t80) REVERT: A 636 LEU cc_start: 0.9219 (tt) cc_final: 0.8938 (pp) REVERT: A 1157 MET cc_start: 0.8526 (tpp) cc_final: 0.8295 (tpp) REVERT: A 1166 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7212 (t80) REVERT: A 1224 ASN cc_start: 0.7735 (m110) cc_final: 0.7201 (t0) REVERT: A 1280 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 1330 GLN cc_start: 0.8497 (mt0) cc_final: 0.8134 (mt0) REVERT: A 1341 ASP cc_start: 0.7926 (t0) cc_final: 0.7629 (t0) outliers start: 26 outliers final: 24 residues processed: 152 average time/residue: 0.2075 time to fit residues: 45.6441 Evaluate side-chains 156 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 966 THR Chi-restraints excluded: chain A residue 1017 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1166 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1410 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.094017 restraints weight = 17307.191| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.84 r_work: 0.3018 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9903 Z= 0.261 Angle : 0.569 8.492 13390 Z= 0.283 Chirality : 0.040 0.171 1545 Planarity : 0.003 0.029 1628 Dihedral : 5.935 53.496 1467 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.80 % Allowed : 19.58 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1171 helix: 1.07 (0.19), residues: 745 sheet: -1.06 (0.53), residues: 75 loop : -0.73 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 865 HIS 0.005 0.001 HIS A1085 PHE 0.024 0.001 PHE A 236 TYR 0.011 0.001 TYR A1381 ARG 0.005 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.13 seconds wall clock time: 39 minutes 21.93 seconds (2361.93 seconds total)