Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 22:30:03 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/12_2021/6msm_9230_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/12_2021/6msm_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_9230/12_2021/6msm_9230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/12_2021/6msm_9230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/12_2021/6msm_9230_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6msm_9230/12_2021/6msm_9230_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-1.20rc4-4434/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: {'POV': 5, ' MG': 2, 'CLR': 1, 'ATP': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 145 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: 5.65, per 1000 atoms: 0.58 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 Amimo 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: 4.09 Conformation dependent library (CDL) restraints added in 1.4 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: 1.64 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: 2.98 Time building geometry restraints manager: 4.39 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: 5440 19.02 - 38.03: 320 38.03 - 57.05: 89 57.05 - 76.06: 9 76.06 - 95.08: 3 Dihedral angle restraints: 5861 sinusoidal: 2379 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 5858 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 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. 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 Write .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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.290 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 27.420 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.220 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 13.611 95.076 3609 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 % 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 *********************** 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 : 1.145 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 270 average time/residue: 0.2413 time to fit residues: 86.5373 Evaluate side-chains 132 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 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 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 HIS A1088 ASN ** A1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN A1330 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9903 Z= 0.205 Angle : 0.591 7.172 13390 Z= 0.307 Chirality : 0.041 0.209 1545 Planarity : 0.004 0.091 1628 Dihedral : 7.340 85.113 1349 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 2.12 % 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: -0.70 (0.22), residues: 1171 helix: 0.33 (0.18), residues: 741 sheet: -1.47 (0.59), residues: 69 loop : -1.78 (0.27), residues: 361 *********************** 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 184 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.137 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 181 average time/residue: 0.1887 time to fit residues: 50.4295 Evaluate side-chains 140 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0932 time to fit residues: 3.9153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 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 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: 0.7570 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 9903 Z= 0.226 Angle : 0.551 7.978 13390 Z= 0.282 Chirality : 0.040 0.179 1545 Planarity : 0.004 0.092 1628 Dihedral : 6.399 75.407 1349 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.64 % 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: -0.04 (0.24), residues: 1171 helix: 0.82 (0.19), residues: 742 sheet: -1.32 (0.56), residues: 81 loop : -1.45 (0.29), residues: 348 *********************** 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 164 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.173 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 160 average time/residue: 0.2047 time to fit residues: 47.6080 Evaluate side-chains 133 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1021 time to fit residues: 2.7249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.7604 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 9903 Z= 0.299 Angle : 0.581 9.316 13390 Z= 0.295 Chirality : 0.041 0.192 1545 Planarity : 0.004 0.098 1628 Dihedral : 6.199 80.276 1349 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.83 % 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: 0.05 (0.24), residues: 1171 helix: 0.81 (0.19), residues: 743 sheet: -1.10 (0.55), residues: 84 loop : -1.25 (0.31), residues: 344 *********************** 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 148 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.190 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 145 average time/residue: 0.1945 time to fit residues: 42.4060 Evaluate side-chains 124 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0974 time to fit residues: 3.5150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.0670 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- 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: 0.7577 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 9903 Z= 0.204 Angle : 0.533 7.741 13390 Z= 0.269 Chirality : 0.039 0.178 1545 Planarity : 0.004 0.106 1628 Dihedral : 5.779 82.397 1349 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.96 % 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 (0.25), residues: 1171 helix: 1.02 (0.20), residues: 744 sheet: -1.08 (0.54), residues: 86 loop : -1.18 (0.32), residues: 341 *********************** 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 145 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.107 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 144 average time/residue: 0.1920 time to fit residues: 40.5691 Evaluate side-chains 123 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0861 time to fit residues: 2.0403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** A1042 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9903 Z= 0.214 Angle : 0.541 7.070 13390 Z= 0.271 Chirality : 0.039 0.181 1545 Planarity : 0.003 0.029 1628 Dihedral : 5.632 84.452 1349 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 1.64 % 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: 0.49 (0.25), residues: 1171 helix: 1.14 (0.20), residues: 745 sheet: -1.02 (0.53), residues: 87 loop : -1.02 (0.32), residues: 339 *********************** 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 143 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 138 average time/residue: 0.1912 time to fit residues: 39.6493 Evaluate side-chains 129 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0957 time to fit residues: 2.9498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.110 9903 Z= 0.222 Angle : 0.547 8.344 13390 Z= 0.276 Chirality : 0.039 0.180 1545 Planarity : 0.004 0.114 1628 Dihedral : 5.535 86.968 1349 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.39 % 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: 0.57 (0.25), residues: 1171 helix: 1.19 (0.20), residues: 741 sheet: -0.94 (0.51), residues: 86 loop : -0.96 (0.32), residues: 344 *********************** 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 139 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 1.180 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 137 average time/residue: 0.2003 time to fit residues: 40.7331 Evaluate side-chains 125 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0972 time to fit residues: 1.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.0670 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 9903 Z= 0.183 Angle : 0.543 8.619 13390 Z= 0.268 Chirality : 0.039 0.179 1545 Planarity : 0.004 0.136 1628 Dihedral : 5.350 87.911 1349 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.68 % 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: 0.69 (0.25), residues: 1171 helix: 1.25 (0.20), residues: 743 sheet: -0.81 (0.50), residues: 86 loop : -0.87 (0.33), residues: 342 *********************** 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 147 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.207 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 144 average time/residue: 0.1957 time to fit residues: 42.0578 Evaluate side-chains 132 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1002 time to fit residues: 2.2898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.4980 chunk 109 optimal weight: 0.0670 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 9903 Z= 0.163 Angle : 0.545 8.842 13390 Z= 0.268 Chirality : 0.039 0.176 1545 Planarity : 0.003 0.061 1628 Dihedral : 5.222 88.154 1349 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.29 % 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: 0.74 (0.25), residues: 1171 helix: 1.26 (0.20), residues: 745 sheet: -0.79 (0.49), residues: 86 loop : -0.75 (0.33), residues: 340 *********************** 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 137 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 136 average time/residue: 0.1880 time to fit residues: 39.1679 Evaluate side-chains 128 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0951 time to fit residues: 1.9840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.0040 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 100 optimal weight: 0.0670 chunk 28 optimal weight: 4.9990 overall best weight: 0.7332 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9903 Z= 0.190 Angle : 0.547 9.265 13390 Z= 0.270 Chirality : 0.039 0.176 1545 Planarity : 0.003 0.048 1628 Dihedral : 5.234 89.474 1349 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.48 % 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: 1.21 (0.19), residues: 744 sheet: -0.74 (0.50), residues: 86 loop : -0.74 (0.33), residues: 341 ********************** 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 136 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 136 average time/residue: 0.1987 time to fit residues: 40.6884 Evaluate side-chains 128 residues out of total 1037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3445 time to fit residues: 2.4693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ** 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 = 0.3413 r_free = 0.3413 target = 0.112201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.094081 restraints weight = 17886.609| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.84 r_work: 0.3128 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work: 0.3112 rms_B_bonded: 2.62 restraints_weight: 0.1250 r_work: 0.3103 rms_B_bonded: 2.65 restraints_weight: 0.0625 r_work: 0.3094 rms_B_bonded: 2.71 restraints_weight: 0.0312 r_work: 0.3085 rms_B_bonded: 2.79 restraints_weight: 0.0156 r_work: 0.3076 rms_B_bonded: 2.88 restraints_weight: 0.0078 r_work: 0.3067 rms_B_bonded: 2.98 restraints_weight: 0.0039 r_work: 0.3058 rms_B_bonded: 3.10 restraints_weight: 0.0020 r_work: 0.3048 rms_B_bonded: 3.24 restraints_weight: 0.0010 r_work: 0.3038 rms_B_bonded: 3.39 restraints_weight: 0.0005 r_work: 0.3027 rms_B_bonded: 3.55 restraints_weight: 0.0002 r_work: 0.3016 rms_B_bonded: 3.73 restraints_weight: 0.0001 r_work: 0.3005 rms_B_bonded: 3.93 restraints_weight: 0.0001 r_work: 0.2993 rms_B_bonded: 4.15 restraints_weight: 0.0000 r_work: 0.2981 rms_B_bonded: 4.38 restraints_weight: 0.0000 r_work: 0.2968 rms_B_bonded: 4.64 restraints_weight: 0.0000 r_work: 0.2955 rms_B_bonded: 4.91 restraints_weight: 0.0000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9903 Z= 0.292 Angle : 0.606 8.439 13390 Z= 0.300 Chirality : 0.041 0.183 1545 Planarity : 0.004 0.044 1628 Dihedral : 5.516 86.336 1349 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1171 helix: 1.00 (0.19), residues: 750 sheet: -0.83 (0.50), residues: 86 loop : -0.77 (0.34), residues: 335 =============================================================================== Job complete usr+sys time: 1896.22 seconds wall clock time: 36 minutes 20.83 seconds (2180.83 seconds total)