Starting phenix.real_space_refine on Sun Dec 10 10:03:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/12_2023/7ogr_12886.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/12_2023/7ogr_12886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/12_2023/7ogr_12886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/12_2023/7ogr_12886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/12_2023/7ogr_12886.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogr_12886/12_2023/7ogr_12886.pdb" } resolution = 3.0 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 73 5.16 5 C 9010 2.51 5 N 2432 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 552": "NH1" <-> "NH2" Residue "C ASP 563": "OD1" <-> "OD2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D GLU 248": "OE1" <-> "OE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E ARG 530": "NH1" <-> "NH2" Residue "E ARG 541": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14135 Number of models: 1 Model: "" Number of chains: 7 Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 160 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1527 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 11, 'TRANS': 178} Chain breaks: 1 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1565 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 9, 'TRANS': 187} Chain breaks: 1 Chain: "C" Number of atoms: 4875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4875 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 35, 'TRANS': 576} Chain breaks: 1 Chain: "D" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3023 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 14, 'TRANS': 358} Chain breaks: 2 Chain: "E" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2984 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 16, 'TRANS': 354} Chain breaks: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10491 SG CYS D 288 16.948 82.058 18.253 1.00 82.42 S ATOM 10896 SG CYS D 341 17.363 79.547 21.885 1.00 84.63 S ATOM 10918 SG CYS D 350 19.774 82.408 19.784 1.00 76.18 S ATOM 10939 SG CYS D 353 17.808 83.449 21.085 1.00 67.76 S Time building chain proxies: 7.82, per 1000 atoms: 0.55 Number of scatterers: 14135 At special positions: 0 Unit cell: (107.1, 135.15, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 73 16.00 O 2619 8.00 N 2432 7.00 C 9010 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: 5.01 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 288 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 341 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 353 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 350 " Number of angles added : 6 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3346 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 17 sheets defined 41.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'X' and resid 4 through 12 Processing helix chain 'X' and resid 18 through 25 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.670A pdb=" N GLN A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.664A pdb=" N ASN A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.657A pdb=" N ASN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 430 through 437 removed outlier: 3.604A pdb=" N THR A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.902A pdb=" N ILE A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.604A pdb=" N LEU A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.673A pdb=" N ALA B 322 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.544A pdb=" N ILE B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.532A pdb=" N THR B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.504A pdb=" N ILE B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 380 removed outlier: 3.551A pdb=" N PHE B 377 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 380 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.617A pdb=" N HIS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.809A pdb=" N MET B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.733A pdb=" N GLU B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 4.114A pdb=" N ALA B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 504 through 520 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.647A pdb=" N MET C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.651A pdb=" N GLU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.664A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.676A pdb=" N ARG C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 327 removed outlier: 3.629A pdb=" N TYR C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 312 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 317 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 348 removed outlier: 3.604A pdb=" N ARG C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 422 No H-bonds generated for 'chain 'C' and resid 420 through 422' Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.592A pdb=" N TYR C 434 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.630A pdb=" N ASN C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 removed outlier: 3.696A pdb=" N VAL C 476 " --> pdb=" O ASN C 472 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 478 " --> pdb=" O GLN C 474 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 490 " --> pdb=" O PHE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.581A pdb=" N VAL C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 Processing helix chain 'C' and resid 634 through 640 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 40 through 49 removed outlier: 3.858A pdb=" N LEU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 51 No H-bonds generated for 'chain 'D' and resid 50 through 51' Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.658A pdb=" N HIS D 56 " --> pdb=" O PRO D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.564A pdb=" N HIS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 67 " --> pdb=" O SER D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 92 through 109 removed outlier: 3.536A pdb=" N HIS D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 137 removed outlier: 3.665A pdb=" N LEU D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 4.011A pdb=" N ILE D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.538A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.778A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.515A pdb=" N LEU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 212 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 261 removed outlier: 4.240A pdb=" N THR D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 277 removed outlier: 4.170A pdb=" N ASN D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG D 271 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 273 " --> pdb=" O PHE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.606A pdb=" N LYS D 307 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.631A pdb=" N ILE D 359 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.828A pdb=" N LYS D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 379 " --> pdb=" O MET D 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 40 through 53 removed outlier: 3.784A pdb=" N ILE E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 323 through 337 removed outlier: 4.233A pdb=" N ASN E 327 " --> pdb=" O LYS E 323 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS E 331 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 366 removed outlier: 3.804A pdb=" N LEU E 361 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 removed outlier: 3.523A pdb=" N HIS E 371 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 372 " --> pdb=" O ALA E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 372' Processing helix chain 'E' and resid 394 through 410 Processing helix chain 'E' and resid 417 through 429 Processing helix chain 'E' and resid 488 through 493 Processing helix chain 'E' and resid 518 through 522 removed outlier: 3.574A pdb=" N GLY E 521 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 300 removed outlier: 7.591A pdb=" N ILE A 404 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 297 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 406 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 299 " --> pdb=" O MET A 406 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE A 312 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 395 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 388 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 372 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 296 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 410 through 412 removed outlier: 3.961A pdb=" N TRP B 478 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 68 removed outlier: 3.667A pdb=" N VAL C 67 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.672A pdb=" N THR C 98 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL C 78 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE C 100 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 123 removed outlier: 4.614A pdb=" N HIS C 122 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 188 removed outlier: 6.915A pdb=" N PHE C 185 " --> pdb=" O CYS C 398 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL C 400 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA C 187 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS C 386 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 198 through 206 removed outlier: 6.374A pdb=" N ARG C 370 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 283 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLU C 372 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE C 281 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 374 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 211 through 213 removed outlier: 3.566A pdb=" N VAL C 270 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA C 241 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG C 268 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AB3, first strand: chain 'C' and resid 550 through 552 Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.005A pdb=" N ASN D 4 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU D 30 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR D 6 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 39 " --> pdb=" O HIS D 27 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 294 through 297 removed outlier: 3.517A pdb=" N ALA D 294 " --> pdb=" O PHE D 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 68 removed outlier: 3.756A pdb=" N TYR E 96 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB8, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.199A pdb=" N ILE E 152 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU E 159 " --> pdb=" O ILE E 152 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1275 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: 3.74 Time building geometry restraints manager: 5.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4599 1.34 - 1.46: 3122 1.46 - 1.58: 6606 1.58 - 1.70: 0 1.70 - 1.81: 130 Bond restraints: 14457 Sorted by residual: bond pdb=" N ARG E 541 " pdb=" CA ARG E 541 " ideal model delta sigma weight residual 1.466 1.501 -0.035 1.36e-02 5.41e+03 6.47e+00 bond pdb=" C ASN C 290 " pdb=" N PRO C 291 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.15e+00 bond pdb=" C PHE E 540 " pdb=" N ARG E 541 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.58e-02 4.01e+03 4.08e+00 bond pdb=" C ALA C 141 " pdb=" N PRO C 142 " ideal model delta sigma weight residual 1.337 1.353 -0.016 9.80e-03 1.04e+04 2.67e+00 bond pdb=" CA ASP C 125 " pdb=" CB ASP C 125 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.54e-02 4.22e+03 1.81e+00 ... (remaining 14452 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.92: 493 106.92 - 114.02: 8147 114.02 - 121.12: 6853 121.12 - 128.23: 3987 128.23 - 135.33: 122 Bond angle restraints: 19602 Sorted by residual: angle pdb=" C GLN D 281 " pdb=" N ARG D 282 " pdb=" CA ARG D 282 " ideal model delta sigma weight residual 120.82 127.00 -6.18 1.47e+00 4.63e-01 1.77e+01 angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 110.21 105.81 4.40 1.13e+00 7.83e-01 1.52e+01 angle pdb=" CA GLN C 3 " pdb=" CB GLN C 3 " pdb=" CG GLN C 3 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" C ILE C 239 " pdb=" N PHE C 240 " pdb=" CA PHE C 240 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C VAL B 367 " pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 122.36 127.57 -5.21 1.42e+00 4.96e-01 1.35e+01 ... (remaining 19597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7854 17.85 - 35.71: 714 35.71 - 53.56: 96 53.56 - 71.41: 12 71.41 - 89.26: 10 Dihedral angle restraints: 8686 sinusoidal: 3500 harmonic: 5186 Sorted by residual: dihedral pdb=" CA ALA A 413 " pdb=" C ALA A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PHE E 540 " pdb=" C PHE E 540 " pdb=" N ARG E 541 " pdb=" CA ARG E 541 " ideal model delta harmonic sigma weight residual 180.00 -153.82 -26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ARG E 510 " pdb=" C ARG E 510 " pdb=" N LEU E 511 " pdb=" CA LEU E 511 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 8683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1571 0.046 - 0.092: 442 0.092 - 0.137: 141 0.137 - 0.183: 20 0.183 - 0.229: 3 Chirality restraints: 2177 Sorted by residual: chirality pdb=" CA PHE C 240 " pdb=" N PHE C 240 " pdb=" C PHE C 240 " pdb=" CB PHE C 240 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN C 290 " pdb=" N ASN C 290 " pdb=" C ASN C 290 " pdb=" CB ASN C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASP C 125 " pdb=" N ASP C 125 " pdb=" C ASP C 125 " pdb=" CB ASP C 125 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 2174 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 540 " -0.037 2.00e-02 2.50e+03 7.19e-02 5.16e+01 pdb=" C PHE E 540 " 0.124 2.00e-02 2.50e+03 pdb=" O PHE E 540 " -0.047 2.00e-02 2.50e+03 pdb=" N ARG E 541 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 141 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO C 142 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 255 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO C 256 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 256 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 256 " 0.033 5.00e-02 4.00e+02 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4292 2.83 - 3.35: 11704 3.35 - 3.86: 22749 3.86 - 4.38: 26495 4.38 - 4.90: 45733 Nonbonded interactions: 110973 Sorted by model distance: nonbonded pdb=" OE1 GLU D 166 " pdb=" OG1 THR D 168 " model vdw 2.309 2.440 nonbonded pdb=" O ALA D 161 " pdb=" OG SER D 176 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR C 434 " pdb=" O ILE D 236 " model vdw 2.343 2.440 nonbonded pdb=" OH TYR C 82 " pdb=" O ILE C 281 " model vdw 2.347 2.440 nonbonded pdb=" OH TYR B 480 " pdb=" O PRO B 483 " model vdw 2.355 2.440 ... (remaining 110968 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 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: 0.890 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: 4.410 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 39.630 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.003 0.048 14457 Z= 0.201 Angle : 0.690 10.328 19602 Z= 0.393 Chirality : 0.048 0.229 2177 Planarity : 0.006 0.072 2515 Dihedral : 13.646 89.265 5340 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.14), residues: 1749 helix: -3.84 (0.10), residues: 700 sheet: -1.71 (0.40), residues: 146 loop : -2.72 (0.16), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 445 HIS 0.011 0.001 HIS C 436 PHE 0.028 0.002 PHE E 151 TYR 0.015 0.001 TYR D 311 ARG 0.005 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 318 average time/residue: 1.4345 time to fit residues: 493.3607 Evaluate side-chains 193 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.5478 time to fit residues: 3.7829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 HIS A 311 HIS A 319 GLN A 347 ASN ** A 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN B 342 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 65 HIS C 245 HIS C 345 GLN C 474 GLN D 66 HIS D 71 ASN D 83 ASN D 104 ASN D 127 ASN D 155 HIS D 189 GLN D 208 GLN D 274 GLN D 278 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN E 123 ASN E 537 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14457 Z= 0.182 Angle : 0.545 13.960 19602 Z= 0.281 Chirality : 0.042 0.159 2177 Planarity : 0.004 0.049 2515 Dihedral : 4.883 23.126 1929 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.49 % Allowed : 13.36 % Favored : 84.15 % 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: -3.06 (0.17), residues: 1749 helix: -2.02 (0.16), residues: 691 sheet: -1.04 (0.43), residues: 134 loop : -2.18 (0.17), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 314 HIS 0.005 0.001 HIS C 436 PHE 0.025 0.001 PHE C 240 TYR 0.014 0.001 TYR C 487 ARG 0.005 0.000 ARG D 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 222 average time/residue: 1.3109 time to fit residues: 317.7714 Evaluate side-chains 193 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 7 average time/residue: 0.5668 time to fit residues: 6.9161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 0.0770 chunk 172 optimal weight: 0.0570 chunk 142 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 453 HIS A 471 ASN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN C 474 GLN C 643 ASN D 71 ASN D 104 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14457 Z= 0.154 Angle : 0.507 11.684 19602 Z= 0.260 Chirality : 0.042 0.155 2177 Planarity : 0.004 0.051 2515 Dihedral : 4.632 22.379 1929 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.36 % Allowed : 15.72 % Favored : 81.93 % 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: -2.14 (0.18), residues: 1749 helix: -0.96 (0.19), residues: 691 sheet: -0.60 (0.44), residues: 136 loop : -1.92 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 103 HIS 0.006 0.001 HIS C 436 PHE 0.022 0.001 PHE C 240 TYR 0.012 0.001 TYR D 311 ARG 0.004 0.000 ARG D 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.739 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 11 residues processed: 209 average time/residue: 1.3837 time to fit residues: 315.1062 Evaluate side-chains 184 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.5527 time to fit residues: 4.8962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.0570 chunk 120 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 492 GLN C 3 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS C 463 GLN C 474 GLN D 71 ASN D 104 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14457 Z= 0.127 Angle : 0.480 10.137 19602 Z= 0.246 Chirality : 0.041 0.144 2177 Planarity : 0.003 0.052 2515 Dihedral : 4.341 21.505 1929 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.01 % Allowed : 16.18 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1749 helix: -0.28 (0.20), residues: 691 sheet: -0.34 (0.44), residues: 136 loop : -1.73 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 26 HIS 0.005 0.000 HIS C 436 PHE 0.020 0.001 PHE C 240 TYR 0.015 0.001 TYR C 478 ARG 0.005 0.000 ARG E 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 18 residues processed: 213 average time/residue: 1.2886 time to fit residues: 300.7462 Evaluate side-chains 194 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 10 residues processed: 8 average time/residue: 0.6529 time to fit residues: 8.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 388 GLN A 471 ASN B 342 GLN B 521 GLN C 3 GLN C 37 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS C 463 GLN C 474 GLN C 538 ASN D 13 ASN D 71 ASN D 104 ASN D 208 GLN D 274 GLN D 312 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14457 Z= 0.346 Angle : 0.645 11.370 19602 Z= 0.329 Chirality : 0.047 0.186 2177 Planarity : 0.004 0.047 2515 Dihedral : 5.176 24.437 1929 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.47 % Allowed : 16.63 % Favored : 79.90 % 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: -1.74 (0.19), residues: 1749 helix: -0.56 (0.19), residues: 700 sheet: -0.41 (0.42), residues: 141 loop : -1.77 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 240 HIS 0.010 0.001 HIS C 436 PHE 0.030 0.002 PHE C 240 TYR 0.023 0.002 TYR C 217 ARG 0.009 0.001 ARG E 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 175 time to evaluate : 1.584 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 21 residues processed: 210 average time/residue: 1.3331 time to fit residues: 306.5953 Evaluate side-chains 183 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.603 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 6 average time/residue: 0.5194 time to fit residues: 5.8855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.0470 chunk 41 optimal weight: 0.1980 chunk 170 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 481 HIS B 492 GLN C 3 GLN C 474 GLN D 13 ASN D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14457 Z= 0.139 Angle : 0.504 9.315 19602 Z= 0.260 Chirality : 0.042 0.154 2177 Planarity : 0.003 0.050 2515 Dihedral : 4.569 23.437 1929 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.88 % Allowed : 18.86 % Favored : 78.26 % 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: -1.20 (0.20), residues: 1749 helix: 0.06 (0.20), residues: 684 sheet: -0.16 (0.44), residues: 132 loop : -1.57 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 397 HIS 0.005 0.001 HIS C 436 PHE 0.023 0.001 PHE C 240 TYR 0.013 0.001 TYR D 311 ARG 0.009 0.000 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 209 average time/residue: 1.2759 time to fit residues: 292.6852 Evaluate side-chains 193 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 6 average time/residue: 0.8480 time to fit residues: 7.9957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 124 optimal weight: 0.0060 chunk 96 optimal weight: 0.0570 chunk 143 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 471 ASN B 481 HIS B 492 GLN C 3 GLN C 474 GLN D 71 ASN D 208 GLN D 274 GLN ** D 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14457 Z= 0.135 Angle : 0.497 9.125 19602 Z= 0.254 Chirality : 0.041 0.163 2177 Planarity : 0.003 0.052 2515 Dihedral : 4.291 21.655 1929 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.16 % Allowed : 19.71 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1749 helix: 0.35 (0.21), residues: 691 sheet: 0.07 (0.44), residues: 129 loop : -1.50 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 26 HIS 0.005 0.001 HIS C 436 PHE 0.021 0.001 PHE C 240 TYR 0.016 0.001 TYR C 478 ARG 0.007 0.000 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 206 average time/residue: 1.3114 time to fit residues: 295.6971 Evaluate side-chains 186 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.2189 time to fit residues: 3.2090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 52.4303 > 50: distance: 43 - 47: 8.766 distance: 47 - 48: 14.258 distance: 48 - 49: 12.216 distance: 48 - 51: 12.668 distance: 49 - 50: 23.959 distance: 49 - 53: 11.808 distance: 51 - 52: 16.588 distance: 53 - 54: 22.356 distance: 54 - 55: 13.923 distance: 54 - 57: 10.554 distance: 55 - 56: 36.010 distance: 55 - 67: 28.776 distance: 57 - 58: 10.741 distance: 58 - 59: 12.042 distance: 60 - 62: 11.874 distance: 60 - 63: 5.222 distance: 61 - 62: 8.473 distance: 62 - 64: 9.740 distance: 63 - 65: 5.760 distance: 64 - 66: 6.070 distance: 65 - 66: 6.032 distance: 67 - 68: 18.644 distance: 68 - 69: 29.907 distance: 68 - 71: 16.849 distance: 69 - 70: 38.674 distance: 69 - 79: 35.157 distance: 70 - 94: 30.679 distance: 71 - 72: 10.215 distance: 72 - 73: 6.984 distance: 72 - 74: 6.310 distance: 73 - 75: 15.464 distance: 74 - 76: 7.714 distance: 75 - 77: 9.554 distance: 76 - 77: 9.973 distance: 77 - 78: 13.546 distance: 79 - 80: 19.257 distance: 79 - 85: 20.781 distance: 80 - 81: 18.739 distance: 80 - 83: 17.841 distance: 81 - 82: 7.125 distance: 81 - 86: 9.945 distance: 83 - 84: 27.586 distance: 84 - 85: 23.531 distance: 86 - 87: 12.863 distance: 87 - 88: 11.595 distance: 87 - 90: 31.496 distance: 88 - 89: 27.425 distance: 88 - 94: 16.599 distance: 90 - 91: 10.206 distance: 91 - 92: 19.774 distance: 91 - 93: 42.504 distance: 94 - 95: 9.296 distance: 95 - 96: 14.828 distance: 95 - 98: 30.326 distance: 96 - 97: 19.232 distance: 96 - 103: 15.942 distance: 98 - 99: 9.562 distance: 99 - 100: 9.460 distance: 100 - 101: 4.999 distance: 101 - 102: 27.731 distance: 103 - 104: 12.894 distance: 104 - 105: 7.973 distance: 104 - 107: 7.212 distance: 105 - 106: 26.464 distance: 105 - 113: 13.275 distance: 107 - 108: 27.169 distance: 108 - 109: 10.294 distance: 108 - 110: 10.652 distance: 109 - 111: 14.600 distance: 110 - 112: 22.795 distance: 111 - 112: 8.600 distance: 113 - 114: 17.658 distance: 114 - 115: 5.059 distance: 114 - 117: 9.144 distance: 115 - 116: 18.949 distance: 115 - 125: 21.637 distance: 117 - 118: 7.608 distance: 118 - 119: 13.042 distance: 118 - 120: 9.978 distance: 119 - 121: 17.862 distance: 120 - 122: 14.729 distance: 121 - 123: 23.105 distance: 122 - 123: 15.091 distance: 123 - 124: 8.162 distance: 125 - 126: 16.880 distance: 126 - 127: 9.823 distance: 126 - 129: 12.574 distance: 127 - 128: 22.001 distance: 127 - 134: 13.770 distance: 129 - 130: 9.478 distance: 130 - 131: 5.860 distance: 131 - 132: 23.258 distance: 132 - 133: 10.998 distance: 134 - 135: 7.670 distance: 135 - 136: 26.829 distance: 135 - 138: 19.179 distance: 136 - 137: 11.254 distance: 136 - 142: 20.658 distance: 138 - 139: 16.336 distance: 139 - 140: 19.412 distance: 139 - 141: 39.837