Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 16:47:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/04_2023/7jpt_22422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/04_2023/7jpt_22422.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/7jpt_22422/04_2023/7jpt_22422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/04_2023/7jpt_22422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/04_2023/7jpt_22422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpt_22422/04_2023/7jpt_22422.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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6576 2.51 5 N 1728 2.21 5 O 1850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ASP 771": "OD1" <-> "OD2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ARG 778": "NH1" <-> "NH2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A ASP 978": "OD1" <-> "OD2" Residue "A TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1027": "OD1" <-> "OD2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A ASP 1143": "OD1" <-> "OD2" Residue "A GLU 1171": "OE1" <-> "OE2" Residue "A PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1196": "OD1" <-> "OD2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A PHE 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1372": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10220 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10153 Classifications: {'peptide': 1327} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 1260} Chain breaks: 5 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 865 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 24, 'TYR:plan': 5, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 2, 'GLU:plan': 47, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 500 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.70, per 1000 atoms: 0.56 Number of scatterers: 10220 At special positions: 0 Unit cell: (86.92, 99.64, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1850 8.00 N 1728 7.00 C 6576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 100 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 332 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 623 " distance=2.03 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 678 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 930 " distance=2.03 Simple disulfide: pdb=" SG CYS A 904 " - pdb=" SG CYS A 922 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1060 " - pdb=" SG CYS A1080 " distance=2.03 Simple disulfide: pdb=" SG CYS A1131 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A1197 " - pdb=" SG CYS A1211 " distance=2.03 Simple disulfide: pdb=" SG CYS A1239 " - pdb=" SG CYS A1255 " distance=2.03 Simple disulfide: pdb=" SG CYS A1277 " - pdb=" SG CYS A1380 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A1801 " - " ASN A1253 " " NAG B 1 " - " ASN A1076 " Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 28 sheets defined 19.0% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 removed outlier: 4.017A pdb=" N ASP A 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.800A pdb=" N GLN A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.599A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.771A pdb=" N VAL A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 3.557A pdb=" N GLU A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 removed outlier: 4.357A pdb=" N GLU A 505 " --> pdb=" O PRO A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 534 through 549 Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.540A pdb=" N LEU A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 702 removed outlier: 4.104A pdb=" N ILE A 694 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 852 through 867 Processing helix chain 'A' and resid 973 through 983 removed outlier: 3.968A pdb=" N ASP A 978 " --> pdb=" O SER A 974 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR A 983 " --> pdb=" O THR A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1003 removed outlier: 3.604A pdb=" N GLN A 996 " --> pdb=" O SER A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1123 through 1134 Processing helix chain 'A' and resid 1143 through 1158 Processing helix chain 'A' and resid 1268 through 1281 removed outlier: 3.719A pdb=" N HIS A1274 " --> pdb=" O GLN A1270 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1281 " --> pdb=" O CYS A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1304 removed outlier: 3.605A pdb=" N TYR A1304 " --> pdb=" O GLU A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1322 removed outlier: 3.689A pdb=" N LYS A1321 " --> pdb=" O TYR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1368 Processing helix chain 'A' and resid 1369 through 1375 removed outlier: 3.598A pdb=" N HIS A1375 " --> pdb=" O TYR A1371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.573A pdb=" N ARG A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 162 removed outlier: 6.479A pdb=" N ILE A 208 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 162 " --> pdb=" O TRP A 206 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TRP A 206 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 238 removed outlier: 3.993A pdb=" N ASN A 233 " --> pdb=" O TYR A 338 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR A 338 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN A 235 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N LEU A 336 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 368 removed outlier: 3.853A pdb=" N TYR A 483 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU A 378 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 481 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 484 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 424 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N LYS A 486 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 15.113A pdb=" N LYS A 426 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 20.743A pdb=" N LYS A 488 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 395 through 396 removed outlier: 3.979A pdb=" N VAL A 484 " --> pdb=" O TRP A 422 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLY A 424 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 10.205A pdb=" N LYS A 486 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 15.113A pdb=" N LYS A 426 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 20.743A pdb=" N LYS A 488 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 421 " --> pdb=" O TYR A 465 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 423 " --> pdb=" O VAL A 463 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 463 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 425 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 461 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N CYS A 462 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 571 removed outlier: 4.541A pdb=" N VAL A 598 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 655 through 660 removed outlier: 3.932A pdb=" N PHE A 780 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 716 removed outlier: 4.923A pdb=" N ALA A 753 " --> pdb=" O ILE A 713 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 823 through 831 removed outlier: 7.722A pdb=" N ASP A 828 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N LEU A 926 " --> pdb=" O ASP A 828 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB9, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AC1, first strand: chain 'A' and resid 956 through 958 Processing sheet with id=AC2, first strand: chain 'A' and resid 970 through 972 Processing sheet with id=AC3, first strand: chain 'A' and resid 1009 through 1010 Processing sheet with id=AC4, first strand: chain 'A' and resid 1009 through 1010 Processing sheet with id=AC5, first strand: chain 'A' and resid 1108 through 1110 Processing sheet with id=AC6, first strand: chain 'A' and resid 1161 through 1162 Processing sheet with id=AC7, first strand: chain 'A' and resid 1165 through 1167 Processing sheet with id=AC8, first strand: chain 'A' and resid 1249 through 1250 Processing sheet with id=AC9, first strand: chain 'A' and resid 1258 through 1259 removed outlier: 3.842A pdb=" N LEU A1378 " --> pdb=" O ILE A1259 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA A1379 " --> pdb=" O MET A1313 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1316 through 1317 274 hydrogen bonds defined for protein. 705 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: 4.51 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3208 1.35 - 1.47: 2866 1.47 - 1.59: 4381 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 10534 Sorted by residual: bond pdb=" C1 NAG A1802 " pdb=" O5 NAG A1802 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.92e+00 bond pdb=" C THR A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.11e-02 8.12e+03 3.97e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" C1 NAG A1801 " pdb=" O5 NAG A1801 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 10529 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.78: 358 106.78 - 113.60: 5664 113.60 - 120.41: 3692 120.41 - 127.23: 4463 127.23 - 134.04: 199 Bond angle restraints: 14376 Sorted by residual: angle pdb=" C TRP A1025 " pdb=" N THR A1026 " pdb=" CA THR A1026 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 angle pdb=" CA CYS A 485 " pdb=" CB CYS A 485 " pdb=" SG CYS A 485 " ideal model delta sigma weight residual 114.40 120.20 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA LEU A 654 " pdb=" CB LEU A 654 " pdb=" CG LEU A 654 " ideal model delta sigma weight residual 116.30 124.75 -8.45 3.50e+00 8.16e-02 5.83e+00 angle pdb=" N LEU A1172 " pdb=" CA LEU A1172 " pdb=" C LEU A1172 " ideal model delta sigma weight residual 113.18 110.00 3.18 1.33e+00 5.65e-01 5.72e+00 angle pdb=" N THR A 440 " pdb=" CA THR A 440 " pdb=" C THR A 440 " ideal model delta sigma weight residual 114.04 111.18 2.86 1.24e+00 6.50e-01 5.31e+00 ... (remaining 14371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5538 17.70 - 35.41: 431 35.41 - 53.11: 121 53.11 - 70.81: 17 70.81 - 88.52: 9 Dihedral angle restraints: 6116 sinusoidal: 2238 harmonic: 3878 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 -179.27 -87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 0.38 -86.38 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -165.64 79.64 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 6113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1315 0.054 - 0.108: 205 0.108 - 0.162: 34 0.162 - 0.216: 0 0.216 - 0.269: 1 Chirality restraints: 1555 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA CYS A1211 " pdb=" N CYS A1211 " pdb=" C CYS A1211 " pdb=" CB CYS A1211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CB ILE A 737 " pdb=" CA ILE A 737 " pdb=" CG1 ILE A 737 " pdb=" CG2 ILE A 737 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1552 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 967 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 968 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 968 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 968 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 813 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 814 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 814 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 814 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 697 " -0.013 2.00e-02 2.50e+03 1.06e-02 1.95e+00 pdb=" CG PHE A 697 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 697 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 697 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 697 " -0.005 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2673 2.79 - 3.32: 8847 3.32 - 3.85: 16455 3.85 - 4.37: 18978 4.37 - 4.90: 32978 Nonbonded interactions: 79931 Sorted by model distance: nonbonded pdb=" OH TYR A 165 " pdb=" OE1 GLN A1301 " model vdw 2.267 2.440 nonbonded pdb=" O SER A 329 " pdb=" OG SER A 329 " model vdw 2.286 2.440 nonbonded pdb=" O SER A1097 " pdb=" OG SER A1097 " model vdw 2.316 2.440 nonbonded pdb=" OE1 GLU A1195 " pdb=" N ASP A1210 " model vdw 2.318 2.520 nonbonded pdb=" NH1 ARG A 160 " pdb=" OD2 ASP A 161 " model vdw 2.324 2.520 ... (remaining 79926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.53 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 1.880 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.900 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 0.002 0.053 10534 Z= 0.162 Angle : 0.548 8.452 14376 Z= 0.292 Chirality : 0.042 0.269 1555 Planarity : 0.003 0.036 1816 Dihedral : 13.654 88.517 3539 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.16 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.19), residues: 1315 helix: -1.24 (0.30), residues: 208 sheet: -2.36 (0.36), residues: 150 loop : -3.33 (0.16), residues: 957 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 230 average time/residue: 0.2581 time to fit residues: 81.4878 Evaluate side-chains 138 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1005 time to fit residues: 5.1530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 GLN A 510 HIS A 529 ASN A 538 GLN A 542 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN A 993 GLN A1059 HIS A1065 ASN A1084 HIS A1173 ASN A1274 HIS A1306 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 10534 Z= 0.237 Angle : 0.587 8.399 14376 Z= 0.298 Chirality : 0.043 0.209 1555 Planarity : 0.004 0.045 1816 Dihedral : 4.370 26.853 1402 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 4.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.20), residues: 1315 helix: -0.14 (0.34), residues: 211 sheet: -2.08 (0.37), residues: 152 loop : -2.95 (0.17), residues: 952 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 169 average time/residue: 0.2244 time to fit residues: 54.7362 Evaluate side-chains 138 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1040 time to fit residues: 6.5192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.0000 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 HIS A 510 HIS ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 10534 Z= 0.301 Angle : 0.632 7.647 14376 Z= 0.323 Chirality : 0.045 0.202 1555 Planarity : 0.004 0.053 1816 Dihedral : 4.875 33.389 1402 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer Outliers : 4.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.93 (0.21), residues: 1315 helix: 0.34 (0.34), residues: 210 sheet: -1.78 (0.39), residues: 142 loop : -2.73 (0.18), residues: 963 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 27 residues processed: 165 average time/residue: 0.2177 time to fit residues: 52.1668 Evaluate side-chains 139 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1019 time to fit residues: 6.7748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0070 chunk 90 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.6404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1153 GLN A1257 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 10534 Z= 0.287 Angle : 0.616 7.687 14376 Z= 0.315 Chirality : 0.044 0.209 1555 Planarity : 0.004 0.070 1816 Dihedral : 4.963 33.390 1402 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.78 (0.21), residues: 1315 helix: 0.59 (0.35), residues: 212 sheet: -1.91 (0.34), residues: 186 loop : -2.63 (0.19), residues: 917 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 153 average time/residue: 0.2338 time to fit residues: 51.1223 Evaluate side-chains 128 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1026 time to fit residues: 4.2800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 10534 Z= 0.249 Angle : 0.607 7.877 14376 Z= 0.308 Chirality : 0.043 0.199 1555 Planarity : 0.004 0.064 1816 Dihedral : 4.903 32.870 1402 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.64 (0.22), residues: 1315 helix: 0.78 (0.35), residues: 212 sheet: -1.87 (0.34), residues: 191 loop : -2.54 (0.19), residues: 912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 152 average time/residue: 0.2160 time to fit residues: 47.6666 Evaluate side-chains 133 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1044 time to fit residues: 5.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10534 Z= 0.201 Angle : 0.596 7.603 14376 Z= 0.302 Chirality : 0.043 0.183 1555 Planarity : 0.004 0.063 1816 Dihedral : 4.869 32.039 1402 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.53 (0.22), residues: 1315 helix: 0.75 (0.35), residues: 218 sheet: -1.73 (0.35), residues: 181 loop : -2.47 (0.19), residues: 916 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 150 average time/residue: 0.2285 time to fit residues: 49.6097 Evaluate side-chains 128 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1030 time to fit residues: 3.3858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 58 optimal weight: 0.0000 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 10534 Z= 0.220 Angle : 0.605 7.564 14376 Z= 0.306 Chirality : 0.043 0.177 1555 Planarity : 0.004 0.063 1816 Dihedral : 4.879 30.698 1402 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.44 (0.22), residues: 1315 helix: 0.87 (0.36), residues: 218 sheet: -1.63 (0.36), residues: 179 loop : -2.43 (0.19), residues: 918 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 137 average time/residue: 0.2382 time to fit residues: 46.8854 Evaluate side-chains 122 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1080 time to fit residues: 2.4538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 ASN A1278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10534 Z= 0.218 Angle : 0.615 11.742 14376 Z= 0.309 Chirality : 0.044 0.280 1555 Planarity : 0.004 0.069 1816 Dihedral : 4.901 30.426 1402 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.33 (0.22), residues: 1315 helix: 1.07 (0.36), residues: 212 sheet: -1.59 (0.36), residues: 177 loop : -2.36 (0.19), residues: 926 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 127 average time/residue: 0.2302 time to fit residues: 41.9859 Evaluate side-chains 122 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0948 time to fit residues: 2.4329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A1065 ASN A1278 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 10534 Z= 0.356 Angle : 0.707 11.279 14376 Z= 0.357 Chirality : 0.047 0.223 1555 Planarity : 0.004 0.073 1816 Dihedral : 5.363 32.271 1402 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % 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: -2.54 (0.22), residues: 1315 helix: 0.76 (0.36), residues: 212 sheet: -1.63 (0.35), residues: 185 loop : -2.49 (0.19), residues: 918 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 129 average time/residue: 0.2316 time to fit residues: 43.2338 Evaluate side-chains 116 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1061 time to fit residues: 2.4540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.102 10534 Z= 0.434 Angle : 0.754 11.685 14376 Z= 0.384 Chirality : 0.048 0.230 1555 Planarity : 0.005 0.073 1816 Dihedral : 5.657 33.294 1402 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.16 % Twisted Proline : 1.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1315 helix: 0.52 (0.36), residues: 211 sheet: -1.61 (0.35), residues: 186 loop : -2.59 (0.19), residues: 918 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2630 Ramachandran restraints generated. 1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 119 average time/residue: 0.2431 time to fit residues: 41.2819 Evaluate side-chains 109 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1023 time to fit residues: 2.1418 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 70.3909 > 50: distance: 56 - 58: 26.575 distance: 58 - 59: 38.499 distance: 59 - 60: 56.132 distance: 59 - 62: 42.141 distance: 60 - 61: 36.656 distance: 60 - 69: 51.201 distance: 62 - 63: 54.139 distance: 63 - 64: 30.453 distance: 64 - 65: 11.363 distance: 65 - 66: 10.323 distance: 66 - 67: 19.530 distance: 66 - 68: 15.123 distance: 69 - 70: 48.665 distance: 69 - 75: 32.124 distance: 70 - 71: 46.638 distance: 70 - 73: 51.675 distance: 71 - 72: 27.791 distance: 71 - 76: 6.627 distance: 73 - 74: 26.576 distance: 74 - 75: 11.867 distance: 76 - 77: 35.682 distance: 77 - 78: 41.985 distance: 77 - 80: 31.392 distance: 78 - 79: 9.359 distance: 78 - 82: 47.067 distance: 80 - 81: 49.116 distance: 81 - 201: 24.603 distance: 82 - 83: 39.243 distance: 83 - 84: 68.021 distance: 83 - 86: 67.266 distance: 84 - 85: 57.683 distance: 84 - 91: 19.569 distance: 86 - 87: 46.096 distance: 87 - 88: 31.695 distance: 88 - 89: 20.915 distance: 88 - 90: 11.338 distance: 91 - 92: 37.045 distance: 92 - 93: 63.854 distance: 92 - 95: 49.841 distance: 93 - 94: 40.225 distance: 93 - 102: 6.618 distance: 95 - 96: 55.429 distance: 96 - 97: 28.530 distance: 96 - 98: 12.432 distance: 97 - 99: 41.271 distance: 98 - 100: 19.405 distance: 99 - 101: 53.718 distance: 100 - 101: 53.943 distance: 102 - 103: 53.732 distance: 102 - 108: 46.852 distance: 103 - 104: 56.256 distance: 103 - 106: 55.710 distance: 104 - 105: 41.136 distance: 104 - 109: 38.308 distance: 106 - 107: 39.150 distance: 107 - 108: 35.907 distance: 109 - 110: 32.652 distance: 109 - 172: 34.160 distance: 110 - 111: 33.880 distance: 110 - 113: 24.870 distance: 111 - 112: 40.249 distance: 111 - 120: 20.290 distance: 112 - 169: 30.623 distance: 113 - 114: 9.086 distance: 114 - 115: 26.683 distance: 114 - 116: 16.316 distance: 115 - 117: 14.641 distance: 116 - 118: 14.686 distance: 117 - 119: 17.050 distance: 118 - 119: 10.550 distance: 120 - 121: 26.448 distance: 121 - 122: 46.316 distance: 121 - 124: 4.210 distance: 122 - 123: 48.042 distance: 122 - 128: 47.433 distance: 124 - 125: 37.761 distance: 125 - 126: 36.368 distance: 125 - 127: 22.288 distance: 128 - 129: 20.688 distance: 128 - 151: 21.347 distance: 129 - 130: 57.443 distance: 129 - 132: 14.958 distance: 130 - 131: 68.834 distance: 130 - 136: 40.825 distance: 131 - 148: 37.498 distance: 132 - 133: 38.249 distance: 132 - 134: 37.613 distance: 133 - 135: 46.812 distance: 136 - 137: 3.297 distance: 137 - 138: 66.421 distance: 137 - 140: 8.436 distance: 138 - 139: 39.137 distance: 138 - 144: 35.171 distance: 140 - 141: 26.074 distance: 141 - 142: 48.850 distance: 141 - 143: 8.678