Starting phenix.real_space_refine on Mon Aug 5 16:24:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/08_2024/7rzw_24780.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/08_2024/7rzw_24780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/08_2024/7rzw_24780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/08_2024/7rzw_24780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/08_2024/7rzw_24780.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzw_24780/08_2024/7rzw_24780.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 105 5.16 5 C 8675 2.51 5 N 2336 2.21 5 O 2500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 582": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 876": "NH1" <-> "NH2" Residue "A ARG 920": "NH1" <-> "NH2" Residue "A GLU 960": "OE1" <-> "OE2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A ARG 1057": "NH1" <-> "NH2" Residue "A GLU 1086": "OE1" <-> "OE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1140": "NH1" <-> "NH2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B ARG 352": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 582": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B ARG 890": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B GLU 954": "OE1" <-> "OE2" Residue "B ARG 978": "NH1" <-> "NH2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B ARG 1102": "NH1" <-> "NH2" Residue "B ARG 1122": "NH1" <-> "NH2" Residue "B ARG 1136": "NH1" <-> "NH2" Residue "B GLU 1137": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6749 Classifications: {'peptide': 859} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 821} Chain breaks: 5 Chain: "B" Number of atoms: 6781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 6781 Classifications: {'peptide': 864} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 826} Chain breaks: 4 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.85, per 1000 atoms: 0.58 Number of scatterers: 13616 At special positions: 0 Unit cell: (124.509, 119.364, 113.19, 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 105 16.00 O 2500 8.00 N 2336 7.00 C 8675 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.07 Conformation dependent library (CDL) restraints added in 2.5 seconds 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3226 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 18 sheets defined 41.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.570A pdb=" N GLN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.136A pdb=" N PHE A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.527A pdb=" N VAL A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 247 removed outlier: 3.965A pdb=" N LEU A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 269 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 411 through 456 removed outlier: 3.871A pdb=" N LEU A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 4.369A pdb=" N VAL A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 509 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 600 through 621 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 848 through 863 removed outlier: 3.900A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 920 removed outlier: 3.792A pdb=" N GLN A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 939 Processing helix chain 'A' and resid 939 through 954 Processing helix chain 'A' and resid 959 through 983 removed outlier: 3.722A pdb=" N GLN A 975 " --> pdb=" O SER A 971 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE A 976 " --> pdb=" O CYS A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1007 removed outlier: 3.573A pdb=" N ILE A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1020 removed outlier: 3.619A pdb=" N ARG A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1058 removed outlier: 3.513A pdb=" N ILE A1044 " --> pdb=" O ASP A1040 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A1058 " --> pdb=" O SER A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 3.650A pdb=" N VAL A1101 " --> pdb=" O PRO A1097 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1128 removed outlier: 3.644A pdb=" N LEU A1125 " --> pdb=" O CYS A1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.826A pdb=" N SER B 165 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.725A pdb=" N ILE B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.310A pdb=" N LEU B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.697A pdb=" N SER B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 3.698A pdb=" N VAL B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 355 through 364 Processing helix chain 'B' and resid 411 through 454 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.593A pdb=" N GLY B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 removed outlier: 3.548A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 474' Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 600 through 620 removed outlier: 3.760A pdb=" N LYS B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 821 Processing helix chain 'B' and resid 824 through 829 Processing helix chain 'B' and resid 848 through 862 Processing helix chain 'B' and resid 908 through 953 removed outlier: 4.509A pdb=" N ASP B 922 " --> pdb=" O GLN B 918 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 923 " --> pdb=" O ARG B 919 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 926 " --> pdb=" O ASP B 922 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 927 " --> pdb=" O THR B 923 " (cutoff:3.500A) Proline residue: B 942 - end of helix Processing helix chain 'B' and resid 959 through 980 Processing helix chain 'B' and resid 1001 through 1021 removed outlier: 3.963A pdb=" N VAL B1005 " --> pdb=" O PHE B1001 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B1015 " --> pdb=" O SER B1011 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU B1016 " --> pdb=" O GLN B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1058 Processing helix chain 'B' and resid 1097 through 1107 removed outlier: 3.574A pdb=" N VAL B1101 " --> pdb=" O PRO B1097 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B1107 " --> pdb=" O ASP B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1112 through 1128 removed outlier: 3.832A pdb=" N LEU B1125 " --> pdb=" O CYS B1121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.651A pdb=" N ARG A 129 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA A 122 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 190 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.651A pdb=" N ARG A 129 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA A 122 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 303 removed outlier: 6.227A pdb=" N VAL A 275 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 289 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 273 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP A 397 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 375 " --> pdb=" O TRP A 397 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 399 " --> pdb=" O MET A 373 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 401 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 371 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS A 403 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 369 " --> pdb=" O HIS A 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 491 removed outlier: 3.573A pdb=" N ASP A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 515 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 783 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER A 517 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 560 through 564 Processing sheet with id=AA7, first strand: chain 'A' and resid 810 through 813 removed outlier: 6.290A pdb=" N ALA A 803 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TRP A 813 " --> pdb=" O ILE A 801 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE A 801 " --> pdb=" O TRP A 813 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA A 887 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASP A 867 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 998 through 1000 removed outlier: 3.912A pdb=" N PHE A1000 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1037 " --> pdb=" O PHE A1000 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1023 through 1027 removed outlier: 3.703A pdb=" N VAL A1065 " --> pdb=" O GLN A1023 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A1027 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1071 through 1075 Processing sheet with id=AB2, first strand: chain 'B' and resid 113 through 114 removed outlier: 6.357A pdb=" N MET B 120 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 190 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 302 through 303 removed outlier: 5.355A pdb=" N VAL B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 277 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 288 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N TRP B 397 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 375 " --> pdb=" O TRP B 397 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 399 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET B 373 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 302 through 303 removed outlier: 5.355A pdb=" N VAL B 286 " --> pdb=" O LYS B 277 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 277 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 288 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB6, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AB7, first strand: chain 'B' and resid 810 through 813 removed outlier: 3.667A pdb=" N GLU B 812 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA B 887 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASP B 867 " --> pdb=" O ALA B 887 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1066 through 1068 removed outlier: 3.593A pdb=" N LYS B1074 " --> pdb=" O ALA B1082 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1066 through 1068 removed outlier: 3.682A pdb=" N GLU B1148 " --> pdb=" O ILE B1083 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B1085 " --> pdb=" O ILE B1146 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1929 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3878 1.34 - 1.45: 2307 1.45 - 1.57: 7534 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 13887 Sorted by residual: bond pdb=" CAO O6E A1201 " pdb=" CBO O6E A1201 " ideal model delta sigma weight residual 1.397 1.528 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" CAO O6E B1201 " pdb=" CBO O6E B1201 " ideal model delta sigma weight residual 1.397 1.517 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.530 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CAV O6E B1201 " pdb=" NAE O6E B1201 " ideal model delta sigma weight residual 1.374 1.456 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" CAY O6E A1201 " pdb=" NAN O6E A1201 " ideal model delta sigma weight residual 1.346 1.423 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 13882 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.86: 342 105.86 - 113.06: 7366 113.06 - 120.26: 5342 120.26 - 127.46: 5578 127.46 - 134.66: 142 Bond angle restraints: 18770 Sorted by residual: angle pdb=" C CYS A 842 " pdb=" N MET A 843 " pdb=" CA MET A 843 " ideal model delta sigma weight residual 121.56 127.70 -6.14 1.56e+00 4.11e-01 1.55e+01 angle pdb=" N MET A 843 " pdb=" CA MET A 843 " pdb=" C MET A 843 " ideal model delta sigma weight residual 110.42 115.85 -5.43 1.46e+00 4.69e-01 1.38e+01 angle pdb=" C ASP B 281 " pdb=" N GLU B 282 " pdb=" CA GLU B 282 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N GLY B 846 " pdb=" CA GLY B 846 " pdb=" C GLY B 846 " ideal model delta sigma weight residual 115.22 119.80 -4.58 1.27e+00 6.20e-01 1.30e+01 angle pdb=" C SER B1107 " pdb=" N SER B1108 " pdb=" CA SER B1108 " ideal model delta sigma weight residual 124.82 131.20 -6.38 1.78e+00 3.16e-01 1.28e+01 ... (remaining 18765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7477 17.98 - 35.95: 772 35.95 - 53.93: 163 53.93 - 71.91: 28 71.91 - 89.89: 16 Dihedral angle restraints: 8456 sinusoidal: 3478 harmonic: 4978 Sorted by residual: dihedral pdb=" CA GLU A1031 " pdb=" C GLU A1031 " pdb=" N ILE A1032 " pdb=" CA ILE A1032 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A1034 " pdb=" C SER A1034 " pdb=" N ILE A1035 " pdb=" CA ILE A1035 " ideal model delta harmonic sigma weight residual -180.00 -156.69 -23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET A1128 " pdb=" C MET A1128 " pdb=" N ASN A1129 " pdb=" CA ASN A1129 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1670 0.066 - 0.133: 365 0.133 - 0.199: 45 0.199 - 0.265: 18 0.265 - 0.331: 3 Chirality restraints: 2101 Sorted by residual: chirality pdb=" CG LEU B 187 " pdb=" CB LEU B 187 " pdb=" CD1 LEU B 187 " pdb=" CD2 LEU B 187 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA PHE B 838 " pdb=" N PHE B 838 " pdb=" C PHE B 838 " pdb=" CB PHE B 838 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU A1116 " pdb=" N LEU A1116 " pdb=" C LEU A1116 " pdb=" CB LEU A1116 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2098 not shown) Planarity restraints: 2413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.207 2.00e-02 2.50e+03 2.11e-01 1.11e+03 pdb=" CAP O6E A1201 " -0.323 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.018 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " -0.186 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " -0.053 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.049 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.475 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " -0.020 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " -0.169 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " -0.198 2.00e-02 2.50e+03 1.98e-01 9.82e+02 pdb=" CAP O6E B1201 " 0.300 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " 0.010 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " 0.178 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " 0.045 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " -0.048 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " -0.446 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " 0.022 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " 0.164 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAQ O6E A1201 " -0.067 2.00e-02 2.50e+03 6.56e-02 5.39e+01 pdb=" CAY O6E A1201 " 0.070 2.00e-02 2.50e+03 pdb=" CBJ O6E A1201 " 0.072 2.00e-02 2.50e+03 pdb=" CBN O6E A1201 " -0.083 2.00e-02 2.50e+03 pdb=" NBP O6E A1201 " 0.009 2.00e-02 2.50e+03 ... (remaining 2410 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4167 2.84 - 3.35: 12408 3.35 - 3.87: 23087 3.87 - 4.38: 26427 4.38 - 4.90: 45454 Nonbonded interactions: 111543 Sorted by model distance: nonbonded pdb=" O THR B 168 " pdb=" OG SER B 172 " model vdw 2.321 3.040 nonbonded pdb=" O SER B 393 " pdb=" OG SER B 393 " model vdw 2.326 3.040 nonbonded pdb=" O VAL B 264 " pdb=" OG1 THR B 268 " model vdw 2.327 3.040 nonbonded pdb=" O ASN B 378 " pdb=" ND2 ASN B 430 " model vdw 2.328 3.120 nonbonded pdb=" O ILE A 470 " pdb=" NE1 TRP A 552 " model vdw 2.347 3.120 ... (remaining 111538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 102 through 220 or resid 227 through 620 or resid 778 thro \ ugh 1151 or resid 1201)) selection = (chain 'B' and (resid 102 through 378 or resid 393 through 986 or resid 993 thro \ ugh 1151 or resid 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.540 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 0.131 13887 Z= 0.408 Angle : 1.006 10.201 18770 Z= 0.553 Chirality : 0.058 0.331 2101 Planarity : 0.010 0.211 2413 Dihedral : 15.417 89.886 5230 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.88 % Allowed : 11.61 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 1701 helix: -1.21 (0.18), residues: 670 sheet: -1.56 (0.27), residues: 344 loop : -2.08 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 563 HIS 0.012 0.002 HIS B1106 PHE 0.041 0.003 PHE B1080 TYR 0.039 0.003 TYR A 487 ARG 0.008 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 301 time to evaluate : 1.527 Fit side-chains REVERT: A 979 ILE cc_start: 0.7161 (mt) cc_final: 0.6817 (mt) REVERT: B 336 GLN cc_start: 0.5618 (pt0) cc_final: 0.5227 (pm20) REVERT: B 431 MET cc_start: 0.7140 (mtp) cc_final: 0.6934 (mtt) REVERT: B 466 GLN cc_start: 0.5340 (tp40) cc_final: 0.5095 (tp40) REVERT: B 483 TYR cc_start: 0.5268 (t80) cc_final: 0.4865 (t80) REVERT: B 611 GLN cc_start: 0.6386 (OUTLIER) cc_final: 0.6107 (pt0) REVERT: B 817 MET cc_start: 0.7298 (mmm) cc_final: 0.7013 (mmm) REVERT: B 823 TRP cc_start: 0.7205 (m100) cc_final: 0.6848 (m100) REVERT: B 940 LYS cc_start: 0.7472 (mttp) cc_final: 0.7108 (tptm) REVERT: B 983 MET cc_start: 0.3602 (ptm) cc_final: 0.3397 (ptm) REVERT: B 1127 LEU cc_start: 0.7764 (tp) cc_final: 0.7297 (mt) outliers start: 13 outliers final: 4 residues processed: 311 average time/residue: 0.2757 time to fit residues: 121.6336 Evaluate side-chains 189 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 184 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 611 GLN Chi-restraints excluded: chain B residue 917 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 155 optimal weight: 0.0040 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 608 HIS A 882 GLN B 959 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13887 Z= 0.188 Angle : 0.652 9.504 18770 Z= 0.333 Chirality : 0.042 0.180 2101 Planarity : 0.005 0.068 2413 Dihedral : 6.775 87.986 1942 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 2.36 % Allowed : 15.26 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 1701 helix: -0.22 (0.19), residues: 698 sheet: -1.42 (0.26), residues: 360 loop : -1.75 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 599 HIS 0.006 0.001 HIS B1106 PHE 0.018 0.002 PHE A 903 TYR 0.014 0.002 TYR A 276 ARG 0.004 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3402 Ramachandran restraints generated. 1701 Oldfield, 0 Emsley, 1701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 204 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 323 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.7076 (ttp) REVERT: A 998 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6815 (pm20) REVERT: A 1072 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5837 (pt) REVERT: A 1076 MET cc_start: 0.7058 (mtp) cc_final: 0.6672 (mtm) REVERT: A 1140 ARG cc_start: 0.6534 (mtt90) cc_final: 0.6017 (mtp180) REVERT: B 291 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7817 (pttp) REVERT: B 336 GLN cc_start: 0.5599 (pt0) cc_final: 0.5370 (pm20) REVERT: B 823 TRP cc_start: 0.7223 (m100) cc_final: 0.6918 (m100) REVERT: B 881 VAL cc_start: 0.7113 (OUTLIER) cc_final: 0.6909 (p) REVERT: B 896 LYS cc_start: 0.5102 (OUTLIER) cc_final: 0.4796 (ptpt) REVERT: B 940 LYS cc_start: 0.7374 (mttp) cc_final: 0.6944 (tptm) REVERT: B 1015 PHE cc_start: 0.7116 (t80) cc_final: 0.6742 (m-80) outliers start: 35 outliers final: 14 residues processed: 227 average time/residue: 0.2714 time to fit residues: 88.5529 Evaluate side-chains 199 residues out of total 1481 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 888 ASN Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 998 GLU Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 896 LYS Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1099 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 52.9485 > 50: distance: 49 - 73: 5.847 distance: 56 - 82: 8.211 distance: 62 - 65: 6.304 distance: 65 - 66: 9.317 distance: 66 - 67: 9.715 distance: 66 - 69: 12.999 distance: 67 - 68: 18.711 distance: 68 - 99: 21.978 distance: 69 - 70: 10.471 distance: 70 - 71: 13.544 distance: 71 - 72: 20.690 distance: 73 - 74: 5.706 distance: 74 - 75: 9.408 distance: 74 - 77: 7.021 distance: 75 - 76: 10.831 distance: 75 - 82: 8.194 distance: 77 - 78: 4.789 distance: 78 - 79: 6.536 distance: 79 - 80: 16.257 distance: 79 - 81: 17.610 distance: 82 - 83: 7.613 distance: 83 - 84: 22.527 distance: 83 - 86: 4.697 distance: 84 - 85: 9.310 distance: 84 - 91: 23.381 distance: 86 - 87: 12.868 distance: 87 - 88: 21.017 distance: 88 - 89: 13.783 distance: 89 - 90: 4.096 distance: 91 - 92: 6.443 distance: 92 - 93: 21.363 distance: 92 - 95: 6.123 distance: 93 - 94: 13.397 distance: 93 - 99: 6.857 distance: 95 - 96: 16.928 distance: 96 - 97: 14.965 distance: 96 - 98: 12.453 distance: 99 - 100: 8.927 distance: 100 - 101: 6.917 distance: 100 - 103: 15.090 distance: 101 - 102: 26.229 distance: 101 - 106: 12.317 distance: 103 - 104: 12.486 distance: 103 - 105: 16.087 distance: 106 - 107: 14.292 distance: 107 - 108: 25.549 distance: 108 - 109: 29.524 distance: 108 - 110: 15.927 distance: 110 - 111: 11.416 distance: 111 - 112: 7.623 distance: 111 - 114: 14.193 distance: 112 - 113: 21.672 distance: 112 - 124: 35.685 distance: 114 - 115: 17.403 distance: 115 - 116: 4.820 distance: 115 - 117: 7.913 distance: 116 - 118: 3.890 distance: 117 - 119: 8.364 distance: 117 - 120: 4.773 distance: 118 - 119: 6.755 distance: 119 - 121: 6.289 distance: 120 - 122: 10.119 distance: 121 - 123: 7.113 distance: 122 - 123: 9.009 distance: 124 - 125: 11.434 distance: 125 - 126: 17.851 distance: 125 - 128: 15.470 distance: 126 - 127: 23.391 distance: 126 - 130: 22.444 distance: 127 - 156: 25.502 distance: 128 - 129: 21.557 distance: 130 - 131: 14.216 distance: 131 - 132: 17.354 distance: 131 - 134: 7.247 distance: 132 - 133: 8.575 distance: 132 - 141: 10.153 distance: 133 - 163: 22.335 distance: 134 - 135: 17.320 distance: 135 - 136: 13.375 distance: 137 - 138: 3.172 distance: 138 - 140: 9.602 distance: 141 - 142: 33.267 distance: 142 - 143: 16.821 distance: 142 - 145: 12.424 distance: 143 - 144: 14.538 distance: 143 - 147: 17.269 distance: 145 - 146: 15.508