Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:43:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155_updated_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155_updated_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155_updated_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eig_28155/12_2022/8eig_28155_updated_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 913": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1425": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9249 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9249 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1147, 9243 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'WJX': 1} Classifications: {'peptide': 1141, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 1110, None: 6} Not linked: pdbres="LYS A1429 " pdbres=" MG A1501 " Not linked: pdbres=" MG A1501 " pdbres=" MG A1502 " Not linked: pdbres=" MG A1502 " pdbres="ATP A1503 " Not linked: pdbres="ATP A1503 " pdbres="ATP A1504 " Not linked: pdbres="ATP A1504 " pdbres="CLR A1505 " Not linked: pdbres="CLR A1505 " pdbres="WJX A1506 " Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1147, 9243 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'WJX': 1} Classifications: {'peptide': 1141, 'undetermined': 6} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 30, 'TRANS': 1110, None: 6} Not linked: pdbres="LYS A1429 " pdbres=" MG A1501 " Not linked: pdbres=" MG A1501 " pdbres=" MG A1502 " Not linked: pdbres=" MG A1502 " pdbres="ATP A1503 " Not linked: pdbres="ATP A1503 " pdbres="ATP A1504 " Not linked: pdbres="ATP A1504 " pdbres="CLR A1505 " Not linked: pdbres="CLR A1505 " pdbres="WJX A1506 " Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 9437 Time building chain proxies: 9.61, per 1000 atoms: 1.04 Number of scatterers: 9249 At special positions: 0 Unit cell: (76.388, 84.5, 140.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 F 3 9.00 O 1629 8.00 N 1530 7.00 C 6032 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: 3.62 Conformation dependent library (CDL) restraints added in 2.6 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 3 sheets defined 60.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.663A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 Proline residue: A 22 - end of helix removed outlier: 3.517A pdb=" N ARG A 25 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 27 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 29 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 removed outlier: 4.174A pdb=" N ARG A 59 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.663A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.663A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 118 No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 121 through 166 removed outlier: 4.207A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix removed outlier: 3.789A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.556A pdb=" N SER A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.663A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 203 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA A 204 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 3.902A pdb=" N ALA A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 212 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 215 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 250 removed outlier: 3.846A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.544A pdb=" N SER A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 278 through 309 removed outlier: 3.754A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.639A pdb=" N LEU A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.982A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 376 removed outlier: 3.548A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.540A pdb=" N LEU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.795A pdb=" N SER A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 532' Processing helix chain 'A' and resid 550 through 563 Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 580 through 589 removed outlier: 3.609A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.853A pdb=" N LYS A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 847 through 854 Processing helix chain 'A' and resid 859 through 883 Processing helix chain 'A' and resid 909 through 926 removed outlier: 3.728A pdb=" N SER A 912 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N TYR A 913 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 914 " --> pdb=" O SER A 911 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP A 924 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 958 removed outlier: 3.757A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 958 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 965 Processing helix chain 'A' and resid 971 through 977 removed outlier: 3.680A pdb=" N ARG A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1011 removed outlier: 4.974A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.599A pdb=" N PHE A 992 " --> pdb=" O PRO A 988 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A1009 " --> pdb=" O ILE A1005 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A1010 " --> pdb=" O ALA A1006 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1018 No H-bonds generated for 'chain 'A' and resid 1015 through 1018' Processing helix chain 'A' and resid 1020 through 1060 removed outlier: 3.943A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.621A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1068 Processing helix chain 'A' and resid 1071 through 1121 removed outlier: 3.524A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU A1104 " --> pdb=" O GLN A1100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1167 removed outlier: 4.519A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A1143 " --> pdb=" O ILE A1139 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A1151 " --> pdb=" O VAL A1147 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A1166 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A1167 " --> pdb=" O VAL A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1257 removed outlier: 4.079A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1285 removed outlier: 3.510A pdb=" N LYS A1284 " --> pdb=" O GLN A1280 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A1285 " --> pdb=" O GLN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1312 through 1322 removed outlier: 4.128A pdb=" N GLU A1321 " --> pdb=" O LYS A1317 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1348 through 1362 Processing helix chain 'A' and resid 1378 through 1390 removed outlier: 4.770A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A1389 " --> pdb=" O ARG A1385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 624 through 628 removed outlier: 7.019A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 615 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG A 600 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 456 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 602 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLY A 458 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1266 through 1269 removed outlier: 5.321A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1421 through 1424 removed outlier: 3.579A pdb=" N PHE A1413 " --> pdb=" O TYR A1424 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A1412 " --> pdb=" O ARG A1239 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A1397 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A1242 " --> pdb=" O VAL A1397 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A1399 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLY A1244 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS A1400 " --> pdb=" O LEU A1369 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1368 " --> pdb=" O GLY A1287 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2854 1.34 - 1.46: 2001 1.46 - 1.58: 4506 1.58 - 1.69: 13 1.69 - 1.81: 77 Bond restraints: 9451 Sorted by residual: bond pdb=" C19 WJX A1506 " pdb=" S WJX A1506 " ideal model delta sigma weight residual 1.822 1.607 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2 WJX A1506 " pdb=" C3 WJX A1506 " ideal model delta sigma weight residual 1.345 1.533 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" C1 WJX A1506 " pdb=" C4 WJX A1506 " ideal model delta sigma weight residual 1.362 1.525 -0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" N WJX A1506 " pdb=" C5 WJX A1506 " ideal model delta sigma weight residual 1.537 1.377 0.160 2.00e-02 2.50e+03 6.44e+01 bond pdb=" C18 WJX A1506 " pdb=" N4 WJX A1506 " ideal model delta sigma weight residual 1.507 1.386 0.121 2.00e-02 2.50e+03 3.69e+01 ... (remaining 9446 not shown) Histogram of bond angle deviations from ideal: 70.03 - 82.83: 4 82.83 - 95.62: 2 95.62 - 108.42: 357 108.42 - 121.22: 10290 121.22 - 134.01: 2160 Bond angle restraints: 12813 Sorted by residual: angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O5' ATP A1503 " ideal model delta sigma weight residual 110.65 70.03 40.62 3.49e+00 8.21e-02 1.35e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O2A ATP A1504 " ideal model delta sigma weight residual 114.42 74.12 40.30 3.53e+00 8.04e-02 1.31e+02 angle pdb=" O1A ATP A1503 " pdb=" PA ATP A1503 " pdb=" O2A ATP A1503 " ideal model delta sigma weight residual 114.42 74.17 40.25 3.53e+00 8.04e-02 1.30e+02 angle pdb=" O1A ATP A1504 " pdb=" PA ATP A1504 " pdb=" O5' ATP A1504 " ideal model delta sigma weight residual 110.65 71.14 39.51 3.49e+00 8.21e-02 1.28e+02 angle pdb=" PB ATP A1503 " pdb=" O3B ATP A1503 " pdb=" PG ATP A1503 " ideal model delta sigma weight residual 139.87 130.44 9.43 1.00e+00 1.00e+00 8.89e+01 ... (remaining 12808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.57: 5348 24.57 - 49.13: 186 49.13 - 73.70: 24 73.70 - 98.26: 6 98.26 - 122.83: 1 Dihedral angle restraints: 5565 sinusoidal: 2246 harmonic: 3319 Sorted by residual: dihedral pdb=" C13 WJX A1506 " pdb=" O WJX A1506 " pdb=" C12 WJX A1506 " pdb=" N3 WJX A1506 " ideal model delta sinusoidal sigma weight residual 170.93 48.10 122.83 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" CA LYS A 532 " pdb=" C LYS A 532 " pdb=" N PHE A 533 " pdb=" CA PHE A 533 " ideal model delta harmonic sigma weight residual 180.00 -159.75 -20.25 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C18 WJX A1506 " pdb=" N4 WJX A1506 " pdb=" S WJX A1506 " pdb=" C19 WJX A1506 " ideal model delta sinusoidal sigma weight residual 147.30 50.99 96.31 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 5562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 866 0.029 - 0.057: 417 0.057 - 0.086: 126 0.086 - 0.114: 54 0.114 - 0.143: 13 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA GLN A1371 " pdb=" N GLN A1371 " pdb=" C GLN A1371 " pdb=" CB GLN A1371 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CB ILE A 177 " pdb=" CA ILE A 177 " pdb=" CG1 ILE A 177 " pdb=" CG2 ILE A 177 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ARG A1259 " pdb=" N ARG A1259 " pdb=" C ARG A1259 " pdb=" CB ARG A1259 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1473 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 WJX A1506 " -0.142 2.00e-02 2.50e+03 9.67e-02 1.17e+02 pdb=" C6 WJX A1506 " 0.109 2.00e-02 2.50e+03 pdb=" N4 WJX A1506 " -0.081 2.00e-02 2.50e+03 pdb=" O1 WJX A1506 " 0.027 2.00e-02 2.50e+03 pdb=" S WJX A1506 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WJX A1506 " -0.056 2.00e-02 2.50e+03 6.65e-02 9.94e+01 pdb=" C18 WJX A1506 " 0.127 2.00e-02 2.50e+03 pdb=" C5 WJX A1506 " -0.012 2.00e-02 2.50e+03 pdb=" C6 WJX A1506 " -0.015 2.00e-02 2.50e+03 pdb=" C7 WJX A1506 " -0.062 2.00e-02 2.50e+03 pdb=" C8 WJX A1506 " -0.063 2.00e-02 2.50e+03 pdb=" C9 WJX A1506 " -0.017 2.00e-02 2.50e+03 pdb=" N1 WJX A1506 " -0.011 2.00e-02 2.50e+03 pdb=" N2 WJX A1506 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O WJX A1506 " 0.014 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" C10 WJX A1506 " -0.004 2.00e-02 2.50e+03 pdb=" C11 WJX A1506 " 0.006 2.00e-02 2.50e+03 pdb=" C12 WJX A1506 " -0.003 2.00e-02 2.50e+03 pdb=" C9 WJX A1506 " 0.022 2.00e-02 2.50e+03 pdb=" N2 WJX A1506 " -0.015 2.00e-02 2.50e+03 pdb=" N3 WJX A1506 " -0.020 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 9 2.49 - 3.09: 6357 3.09 - 3.69: 13023 3.69 - 4.30: 19539 4.30 - 4.90: 31862 Nonbonded interactions: 70790 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O2B ATP A1504 " model vdw 1.883 2.170 nonbonded pdb="MG MG A1501 " pdb=" O3G ATP A1503 " model vdw 2.010 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.117 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3G ATP A1504 " model vdw 2.332 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.354 2.170 ... (remaining 70785 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6032 2.51 5 N 1530 2.21 5 O 1629 1.98 5 F 3 1.80 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 17.990 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 33.250 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.006 0.215 9451 Z= 0.384 Angle : 1.038 40.620 12813 Z= 0.414 Chirality : 0.039 0.143 1476 Planarity : 0.004 0.097 1553 Dihedral : 12.669 122.830 3421 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.44 % Rotamer Outliers : 1.91 % 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: -0.77 (0.23), residues: 1132 helix: 0.14 (0.19), residues: 661 sheet: -1.17 (0.68), residues: 53 loop : -1.37 (0.28), residues: 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 1.087 Fit side-chains outliers start: 19 outliers final: 4 residues processed: 206 average time/residue: 0.2454 time to fit residues: 67.6694 Evaluate side-chains 117 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0806 time to fit residues: 1.9458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.0370 chunk 47 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 186 ASN A 187 ASN A 353 GLN A 369 ASN A 452 GLN A 493 GLN A 958 GLN A 965 ASN A1012 GLN A1100 GLN A1144 GLN A1238 GLN A1268 GLN A1280 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9451 Z= 0.150 Angle : 0.574 11.036 12813 Z= 0.283 Chirality : 0.040 0.139 1476 Planarity : 0.004 0.026 1553 Dihedral : 7.023 117.100 1257 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer Outliers : 1.41 % 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: 0.36 (0.25), residues: 1132 helix: 1.32 (0.20), residues: 679 sheet: -1.08 (0.68), residues: 53 loop : -1.48 (0.28), residues: 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.953 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 150 average time/residue: 0.2322 time to fit residues: 48.0491 Evaluate side-chains 111 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1038 time to fit residues: 2.2188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A1138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9451 Z= 0.198 Angle : 0.561 10.577 12813 Z= 0.277 Chirality : 0.040 0.148 1476 Planarity : 0.004 0.037 1553 Dihedral : 7.022 115.303 1257 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer Outliers : 1.51 % 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: 0.56 (0.25), residues: 1132 helix: 1.55 (0.21), residues: 674 sheet: -0.69 (0.78), residues: 43 loop : -1.54 (0.28), residues: 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.006 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 119 average time/residue: 0.2135 time to fit residues: 36.5615 Evaluate side-chains 111 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0974 time to fit residues: 3.2038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 110 optimal weight: 0.0040 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 9451 Z= 0.140 Angle : 0.508 9.243 12813 Z= 0.252 Chirality : 0.039 0.189 1476 Planarity : 0.003 0.032 1553 Dihedral : 6.869 115.786 1257 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer Outliers : 0.81 % 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: 0.77 (0.25), residues: 1132 helix: 1.75 (0.21), residues: 676 sheet: -0.48 (0.78), residues: 43 loop : -1.54 (0.28), residues: 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.125 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 119 average time/residue: 0.2018 time to fit residues: 35.0769 Evaluate side-chains 108 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.121 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1532 time to fit residues: 2.6650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS A1423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9451 Z= 0.189 Angle : 0.531 8.659 12813 Z= 0.264 Chirality : 0.040 0.130 1476 Planarity : 0.003 0.032 1553 Dihedral : 6.933 116.183 1257 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer Outliers : 1.31 % 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: 1132 helix: 1.70 (0.21), residues: 675 sheet: -0.95 (0.75), residues: 50 loop : -1.54 (0.28), residues: 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.108 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 119 average time/residue: 0.2003 time to fit residues: 34.7838 Evaluate side-chains 112 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1357 time to fit residues: 3.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9451 Z= 0.200 Angle : 0.542 12.272 12813 Z= 0.266 Chirality : 0.040 0.150 1476 Planarity : 0.003 0.031 1553 Dihedral : 7.003 117.663 1257 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer Outliers : 0.60 % 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: 0.68 (0.26), residues: 1132 helix: 1.70 (0.21), residues: 675 sheet: -0.77 (0.75), residues: 50 loop : -1.58 (0.28), residues: 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.243 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.1977 time to fit residues: 33.0004 Evaluate side-chains 107 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1057 time to fit residues: 2.2233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9451 Z= 0.140 Angle : 0.496 9.714 12813 Z= 0.245 Chirality : 0.038 0.150 1476 Planarity : 0.003 0.027 1553 Dihedral : 6.887 115.671 1257 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.46 % Rotamer Outliers : 0.60 % 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: 0.79 (0.26), residues: 1132 helix: 1.80 (0.21), residues: 679 sheet: -0.69 (0.75), residues: 50 loop : -1.61 (0.28), residues: 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.070 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 0.2007 time to fit residues: 33.8672 Evaluate side-chains 109 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1053 time to fit residues: 2.2598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9451 Z= 0.169 Angle : 0.511 8.868 12813 Z= 0.253 Chirality : 0.040 0.246 1476 Planarity : 0.003 0.027 1553 Dihedral : 6.956 114.835 1257 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1132 helix: 1.74 (0.21), residues: 680 sheet: -0.24 (0.67), residues: 70 loop : -1.69 (0.28), residues: 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.062 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 108 average time/residue: 0.1977 time to fit residues: 31.2893 Evaluate side-chains 106 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0950 time to fit residues: 2.1407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.0060 chunk 66 optimal weight: 0.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 9451 Z= 0.130 Angle : 0.493 8.711 12813 Z= 0.242 Chirality : 0.039 0.219 1476 Planarity : 0.003 0.028 1553 Dihedral : 6.879 113.406 1257 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer Outliers : 0.20 % 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 (0.26), residues: 1132 helix: 1.84 (0.21), residues: 680 sheet: -0.24 (0.66), residues: 70 loop : -1.73 (0.28), residues: 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.080 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 111 average time/residue: 0.2087 time to fit residues: 33.5169 Evaluate side-chains 105 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1197 time to fit residues: 2.0524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.9737 > 50: distance: 8 - 28: 7.987 distance: 14 - 37: 13.858 distance: 17 - 21: 9.871 distance: 21 - 22: 4.181 distance: 22 - 23: 5.436 distance: 22 - 25: 7.391 distance: 23 - 24: 11.396 distance: 23 - 28: 4.966 distance: 25 - 26: 9.250 distance: 25 - 27: 23.116 distance: 28 - 29: 5.071 distance: 29 - 30: 9.357 distance: 29 - 32: 10.596 distance: 30 - 31: 4.442 distance: 30 - 37: 4.713 distance: 32 - 33: 5.600 distance: 33 - 34: 8.592 distance: 34 - 35: 3.583 distance: 35 - 36: 9.681 distance: 37 - 38: 10.996 distance: 38 - 39: 4.911 distance: 38 - 41: 13.575 distance: 39 - 40: 5.574 distance: 39 - 42: 3.961 distance: 42 - 43: 16.821 distance: 43 - 44: 7.083 distance: 43 - 46: 21.442 distance: 44 - 45: 13.751 distance: 44 - 54: 28.471 distance: 46 - 47: 10.472 distance: 47 - 48: 11.289 distance: 47 - 49: 7.955 distance: 48 - 50: 3.734 distance: 49 - 51: 4.778 distance: 50 - 52: 7.212 distance: 51 - 52: 7.596 distance: 52 - 53: 19.660 distance: 54 - 55: 35.650 distance: 55 - 56: 23.802 distance: 55 - 58: 33.374 distance: 56 - 57: 26.499 distance: 56 - 60: 10.098 distance: 58 - 59: 19.069 distance: 60 - 61: 9.250 distance: 61 - 62: 10.792 distance: 61 - 64: 10.879 distance: 62 - 63: 15.132 distance: 62 - 74: 8.245 distance: 64 - 65: 8.504 distance: 65 - 66: 4.976 distance: 65 - 67: 3.544 distance: 66 - 68: 6.459 distance: 67 - 69: 6.450 distance: 67 - 70: 8.269 distance: 68 - 69: 5.112 distance: 70 - 72: 3.458 distance: 71 - 73: 5.709 distance: 72 - 73: 5.884 distance: 74 - 75: 5.240 distance: 75 - 78: 8.986 distance: 76 - 77: 5.607 distance: 77 - 105: 12.731 distance: 78 - 79: 7.940 distance: 79 - 80: 9.927 distance: 80 - 81: 13.538 distance: 80 - 82: 8.202 distance: 83 - 84: 7.095 distance: 84 - 85: 3.766 distance: 84 - 87: 10.056 distance: 85 - 86: 6.585 distance: 85 - 92: 3.350 distance: 86 - 114: 6.832 distance: 87 - 88: 10.689 distance: 88 - 89: 15.243 distance: 89 - 90: 11.007 distance: 89 - 91: 11.279 distance: 92 - 93: 5.911 distance: 93 - 94: 5.510 distance: 93 - 96: 8.294 distance: 94 - 95: 18.966 distance: 94 - 97: 3.228 distance: 95 - 123: 18.892 distance: 97 - 98: 8.677 distance: 98 - 101: 7.330 distance: 99 - 105: 5.971 distance: 100 - 129: 4.819 distance: 101 - 102: 6.507 distance: 103 - 104: 13.779