Starting phenix.real_space_refine on Fri Mar 15 06:12:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_0257/03_2024/6hra_0257_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_0257/03_2024/6hra_0257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_0257/03_2024/6hra_0257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_0257/03_2024/6hra_0257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_0257/03_2024/6hra_0257_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_0257/03_2024/6hra_0257_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6968 2.51 5 N 1823 2.21 5 O 1962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 475": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10818 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1413 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 13, 'TRANS': 173} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5047 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 26, 'TRANS': 652} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.96, per 1000 atoms: 0.55 Number of scatterers: 10818 At special positions: 0 Unit cell: (98.164, 113.344, 152.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 61 16.00 P 1 15.00 O 1962 8.00 N 1823 7.00 C 6968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 2.1 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 5 sheets defined 49.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.639A pdb=" N LEU A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 8 " --> pdb=" O GLN A 4 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.534A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.587A pdb=" N CYS A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.738A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.544A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.692A pdb=" N ALA A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 156 removed outlier: 3.627A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.874A pdb=" N ARG A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.618A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 4.377A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.670A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 4.387A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 303 removed outlier: 4.385A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.606A pdb=" N LEU A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.703A pdb=" N VAL A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.844A pdb=" N MET A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 4.028A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 415 through 434 removed outlier: 3.868A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 3.581A pdb=" N VAL A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.446A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.684A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.511A pdb=" N CYS A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.875A pdb=" N ILE A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 538 removed outlier: 3.713A pdb=" N GLY A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.573A pdb=" N PHE C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 19 No H-bonds generated for 'chain 'C' and resid 16 through 19' Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.687A pdb=" N TRP C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.528A pdb=" N LYS C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.606A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 161 removed outlier: 3.845A pdb=" N GLN C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 189 removed outlier: 3.591A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 23 removed outlier: 3.668A pdb=" N THR D 7 " --> pdb=" O ALA D 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 22 removed outlier: 4.249A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 34 through 55 removed outlier: 3.722A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 101 removed outlier: 4.050A pdb=" N ALA B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.056A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 237 removed outlier: 3.822A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 4.105A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.658A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 271 through 284 removed outlier: 4.014A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.876A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.792A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 removed outlier: 3.846A pdb=" N ASP B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.780A pdb=" N ALA B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.661A pdb=" N ILE B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 555 through 565 removed outlier: 4.138A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 562 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 565 " --> pdb=" O VAL B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 594 removed outlier: 4.437A pdb=" N ARG B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.526A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 637 removed outlier: 4.410A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 655 removed outlier: 3.956A pdb=" N ARG B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 Proline residue: B 665 - end of helix removed outlier: 4.260A pdb=" N LYS B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.718A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= D, first strand: chain 'B' and resid 303 through 307 removed outlier: 6.410A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 394 through 396 removed outlier: 4.645A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3056 1.33 - 1.45: 1681 1.45 - 1.57: 6164 1.57 - 1.69: 4 1.69 - 1.81: 110 Bond restraints: 11015 Sorted by residual: bond pdb=" C ASN B 26 " pdb=" N PRO B 27 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.42e+00 bond pdb=" CG LEU A 422 " pdb=" CD2 LEU A 422 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" CB PRO A 425 " pdb=" CG PRO A 425 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.68e+00 bond pdb=" CG1 ILE B 267 " pdb=" CD1 ILE B 267 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.65e+00 bond pdb=" CB VAL B 231 " pdb=" CG2 VAL B 231 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 ... (remaining 11010 not shown) Histogram of bond angle deviations from ideal: 95.60 - 103.28: 126 103.28 - 110.96: 4175 110.96 - 118.64: 4661 118.64 - 126.33: 5868 126.33 - 134.01: 163 Bond angle restraints: 14993 Sorted by residual: angle pdb=" N ILE A 398 " pdb=" CA ILE A 398 " pdb=" C ILE A 398 " ideal model delta sigma weight residual 113.71 105.24 8.47 9.50e-01 1.11e+00 7.94e+01 angle pdb=" N ILE D 24 " pdb=" CA ILE D 24 " pdb=" C ILE D 24 " ideal model delta sigma weight residual 112.29 107.96 4.33 9.40e-01 1.13e+00 2.12e+01 angle pdb=" C PRO B 11 " pdb=" N THR B 12 " pdb=" CA THR B 12 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 angle pdb=" C PHE A 260 " pdb=" CA PHE A 260 " pdb=" CB PHE A 260 " ideal model delta sigma weight residual 111.22 106.62 4.60 1.23e+00 6.61e-01 1.40e+01 angle pdb=" C ASN B 316 " pdb=" N ARG B 317 " pdb=" CA ARG B 317 " ideal model delta sigma weight residual 122.07 127.36 -5.29 1.43e+00 4.89e-01 1.37e+01 ... (remaining 14988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.27: 6240 15.27 - 30.54: 245 30.54 - 45.81: 55 45.81 - 61.09: 6 61.09 - 76.36: 8 Dihedral angle restraints: 6554 sinusoidal: 2446 harmonic: 4108 Sorted by residual: dihedral pdb=" CA VAL B 449 " pdb=" C VAL B 449 " pdb=" N LYS B 450 " pdb=" CA LYS B 450 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASP B 447 " pdb=" C ASP B 447 " pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PHE B 412 " pdb=" C PHE B 412 " pdb=" N PRO B 413 " pdb=" CA PRO B 413 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 6551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1659 0.092 - 0.183: 144 0.183 - 0.275: 5 0.275 - 0.367: 0 0.367 - 0.458: 1 Chirality restraints: 1809 Sorted by residual: chirality pdb=" CB ILE A 368 " pdb=" CA ILE A 368 " pdb=" CG1 ILE A 368 " pdb=" CG2 ILE A 368 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CG LEU A 133 " pdb=" CB LEU A 133 " pdb=" CD1 LEU A 133 " pdb=" CD2 LEU A 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1806 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 447 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 448 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 215 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 216 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 523 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO B 524 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.032 5.00e-02 4.00e+02 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3243 2.81 - 3.39: 11827 3.39 - 3.97: 20568 3.97 - 4.56: 28878 4.56 - 5.14: 41948 Nonbonded interactions: 106464 Sorted by model distance: nonbonded pdb=" OG SER B 175 " pdb=" O GLY B 538 " model vdw 2.227 2.440 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.241 2.440 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.264 2.440 nonbonded pdb=" OG SER B 192 " pdb=" OE1 GLN B 540 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.298 2.440 ... (remaining 106459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 3.580 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.480 Find NCS groups from input model: 0.310 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.007 0.082 11015 Z= 0.435 Angle : 0.926 9.600 14993 Z= 0.488 Chirality : 0.054 0.458 1809 Planarity : 0.007 0.069 1902 Dihedral : 9.853 76.358 3914 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.18 % Allowed : 3.08 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.16), residues: 1439 helix: -4.02 (0.10), residues: 737 sheet: -2.86 (0.50), residues: 70 loop : -2.85 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 364 HIS 0.011 0.002 HIS A 451 PHE 0.035 0.003 PHE A 109 TYR 0.026 0.003 TYR B 587 ARG 0.009 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TYR cc_start: 0.8982 (p90) cc_final: 0.8660 (p90) REVERT: A 458 TYR cc_start: 0.9066 (t80) cc_final: 0.8571 (t80) REVERT: C 5 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7475 (ttt180) REVERT: C 119 GLU cc_start: 0.9232 (mp0) cc_final: 0.8991 (mp0) REVERT: C 130 ASN cc_start: 0.8995 (t0) cc_final: 0.8780 (t0) REVERT: C 189 ASP cc_start: 0.8356 (t0) cc_final: 0.7980 (t70) REVERT: B 131 ILE cc_start: 0.8489 (mm) cc_final: 0.8206 (pt) REVERT: B 317 ARG cc_start: 0.8401 (ptt180) cc_final: 0.8144 (ttt180) REVERT: B 359 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6961 (ptt-90) REVERT: B 448 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8123 (mm) REVERT: B 530 ASP cc_start: 0.7942 (m-30) cc_final: 0.7677 (m-30) REVERT: B 535 MET cc_start: 0.8789 (mmp) cc_final: 0.8249 (mmt) REVERT: B 619 SER cc_start: 0.8949 (m) cc_final: 0.8584 (t) REVERT: B 649 MET cc_start: 0.8375 (ttt) cc_final: 0.8030 (ttt) REVERT: B 669 ILE cc_start: 0.8974 (mm) cc_final: 0.8691 (mm) outliers start: 2 outliers final: 0 residues processed: 255 average time/residue: 0.2376 time to fit residues: 84.3301 Evaluate side-chains 129 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 448 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN A 447 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN B 30 GLN B 80 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN B 554 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11015 Z= 0.206 Angle : 0.624 8.235 14993 Z= 0.316 Chirality : 0.041 0.159 1809 Planarity : 0.005 0.048 1902 Dihedral : 5.735 34.713 1529 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.20 % Allowed : 10.39 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.19), residues: 1439 helix: -2.32 (0.16), residues: 739 sheet: -2.67 (0.47), residues: 90 loop : -2.40 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 167 HIS 0.002 0.001 HIS A 451 PHE 0.027 0.002 PHE C 11 TYR 0.018 0.001 TYR A 381 ARG 0.005 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8822 (mtmm) REVERT: A 71 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.7072 (mtm) REVERT: A 118 TYR cc_start: 0.8948 (p90) cc_final: 0.8648 (p90) REVERT: C 5 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7342 (ttt180) REVERT: C 130 ASN cc_start: 0.8927 (t0) cc_final: 0.8711 (t0) REVERT: C 189 ASP cc_start: 0.8340 (t0) cc_final: 0.8011 (t0) REVERT: B 58 MET cc_start: 0.6561 (ptp) cc_final: 0.6242 (ptp) REVERT: B 317 ARG cc_start: 0.8379 (ptt180) cc_final: 0.8136 (ttt180) REVERT: B 448 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8066 (mm) REVERT: B 515 MET cc_start: 0.8464 (tpp) cc_final: 0.7900 (tpp) REVERT: B 535 MET cc_start: 0.8886 (mmp) cc_final: 0.8369 (mmt) REVERT: B 619 SER cc_start: 0.8961 (m) cc_final: 0.8685 (t) REVERT: B 669 ILE cc_start: 0.9168 (mm) cc_final: 0.8425 (mm) outliers start: 25 outliers final: 10 residues processed: 178 average time/residue: 0.2279 time to fit residues: 57.9649 Evaluate side-chains 142 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 632 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 67.1634 > 50: distance: 61 - 65: 33.018 distance: 65 - 66: 36.043 distance: 66 - 67: 24.969 distance: 66 - 69: 26.210 distance: 67 - 68: 20.309 distance: 67 - 71: 15.596 distance: 69 - 70: 30.605 distance: 71 - 72: 16.343 distance: 72 - 73: 36.616 distance: 72 - 75: 20.431 distance: 73 - 74: 13.133 distance: 73 - 80: 26.945 distance: 75 - 76: 15.507 distance: 76 - 77: 8.912 distance: 77 - 78: 13.844 distance: 77 - 79: 10.399 distance: 80 - 81: 26.397 distance: 81 - 82: 9.021 distance: 81 - 84: 25.575 distance: 82 - 83: 17.164 distance: 82 - 89: 19.136 distance: 84 - 85: 37.546 distance: 85 - 86: 25.602 distance: 86 - 87: 24.375 distance: 86 - 88: 3.774 distance: 89 - 90: 10.924 distance: 89 - 95: 21.374 distance: 90 - 91: 11.382 distance: 90 - 93: 18.572 distance: 91 - 92: 13.886 distance: 91 - 96: 6.998 distance: 93 - 94: 16.583 distance: 94 - 95: 3.469 distance: 96 - 97: 23.996 distance: 97 - 98: 12.351 distance: 97 - 100: 13.416 distance: 98 - 99: 14.647 distance: 98 - 104: 23.737 distance: 100 - 101: 32.964 distance: 101 - 102: 12.187 distance: 101 - 103: 27.976 distance: 104 - 105: 20.168 distance: 105 - 106: 27.806 distance: 105 - 108: 17.989 distance: 106 - 107: 15.678 distance: 106 - 111: 19.597 distance: 108 - 109: 22.440 distance: 108 - 110: 21.491 distance: 111 - 112: 9.839 distance: 112 - 115: 7.611 distance: 113 - 120: 15.434 distance: 115 - 116: 17.577 distance: 116 - 117: 24.975 distance: 117 - 118: 11.327 distance: 118 - 119: 18.360 distance: 120 - 121: 28.669 distance: 121 - 122: 8.848 distance: 121 - 124: 29.147 distance: 122 - 123: 18.565 distance: 124 - 125: 13.641 distance: 125 - 126: 14.879 distance: 125 - 127: 10.276 distance: 126 - 128: 7.677 distance: 127 - 129: 7.572 distance: 128 - 130: 6.483 distance: 129 - 130: 17.805 distance: 130 - 131: 4.425 distance: 132 - 133: 5.350 distance: 133 - 134: 20.008 distance: 133 - 136: 23.021 distance: 134 - 135: 33.186 distance: 134 - 140: 17.365 distance: 136 - 137: 21.293 distance: 136 - 138: 8.138 distance: 137 - 139: 12.370 distance: 140 - 141: 37.080 distance: 141 - 142: 9.968 distance: 142 - 143: 11.886 distance: 142 - 144: 28.938