Starting phenix.real_space_refine on Tue Dec 12 13:46:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/12_2023/6k15_9905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/12_2023/6k15_9905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/12_2023/6k15_9905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/12_2023/6k15_9905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/12_2023/6k15_9905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k15_9905/12_2023/6k15_9905.pdb" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 84 5.16 5 C 13701 2.51 5 N 3632 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 350": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 144": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H ARG 252": "NH1" <-> "NH2" Residue "H PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 84": "NH1" <-> "NH2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ARG 268": "NH1" <-> "NH2" Residue "M ARG 272": "NH1" <-> "NH2" Residue "I TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 400": "NH1" <-> "NH2" Residue "I ARG 468": "NH1" <-> "NH2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 309": "NH1" <-> "NH2" Residue "G ARG 366": "NH1" <-> "NH2" Residue "G ARG 379": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 50": "NH1" <-> "NH2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 202": "NH1" <-> "NH2" Residue "J ARG 258": "NH1" <-> "NH2" Residue "J TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 277": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "X PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 605": "NH1" <-> "NH2" Residue "L ARG 764": "NH1" <-> "NH2" Residue "L ARG 793": "NH1" <-> "NH2" Residue "L PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21486 Number of models: 1 Model: "" Number of chains: 14 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 964 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "H" Number of atoms: 3215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3215 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 13, 'TRANS': 379} Chain breaks: 2 Chain: "D" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2510 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 4 Chain: "M" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3058 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1944 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 3 Chain: "G" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1991 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 233} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3007 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 22, 'TRANS': 342} Chain breaks: 3 Chain: "J" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1814 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "K" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 347 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "X" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Chain: "L" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 7, 'TRANS': 77} Chain breaks: 2 Chain: "H" 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 2484 SG CYS H 260 64.277 108.986 63.012 1.00 83.94 S ATOM 2507 SG CYS H 263 61.868 110.525 60.797 1.00 89.19 S ATOM 2693 SG CYS H 286 64.537 113.050 62.273 1.00 78.89 S Time building chain proxies: 11.74, per 1000 atoms: 0.55 Number of scatterers: 21486 At special positions: 0 Unit cell: (136.96, 170.13, 177.62, 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 84 16.00 O 4068 8.00 N 3632 7.00 C 13701 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: 8.16 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 286 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 263 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 260 " 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5154 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 16 sheets defined 50.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'F' and resid 319 through 343 removed outlier: 3.831A pdb=" N LYS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL F 341 " --> pdb=" O ASP F 337 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU F 342 " --> pdb=" O ARG F 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 416 through 430 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 95 through 102 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'H' and resid 114 through 131 removed outlier: 3.526A pdb=" N LEU H 131 " --> pdb=" O ASN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 144 removed outlier: 3.670A pdb=" N VAL H 142 " --> pdb=" O THR H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 163 Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.782A pdb=" N LYS H 175 " --> pdb=" O PRO H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 247 through 251 removed outlier: 3.849A pdb=" N ASN H 250 " --> pdb=" O GLU H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 289 removed outlier: 3.562A pdb=" N PHE H 287 " --> pdb=" O CYS H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 331 Processing helix chain 'H' and resid 333 through 342 removed outlier: 3.993A pdb=" N HIS H 340 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY H 342 " --> pdb=" O ALA H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 356 removed outlier: 4.059A pdb=" N GLU H 352 " --> pdb=" O GLU H 348 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 368 Processing helix chain 'H' and resid 388 through 401 Processing helix chain 'H' and resid 403 through 405 No H-bonds generated for 'chain 'H' and resid 403 through 405' Processing helix chain 'H' and resid 406 through 483 removed outlier: 4.144A pdb=" N LYS H 413 " --> pdb=" O LYS H 409 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE H 417 " --> pdb=" O LYS H 413 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU H 419 " --> pdb=" O ARG H 415 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA H 427 " --> pdb=" O GLU H 423 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU H 431 " --> pdb=" O ALA H 427 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS H 434 " --> pdb=" O GLN H 430 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET H 437 " --> pdb=" O VAL H 433 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 438 " --> pdb=" O LYS H 434 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS H 439 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS H 446 " --> pdb=" O SER H 442 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP H 449 " --> pdb=" O THR H 445 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 450 " --> pdb=" O LYS H 446 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR H 452 " --> pdb=" O CYS H 448 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU H 455 " --> pdb=" O GLU H 451 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL H 462 " --> pdb=" O LYS H 458 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS H 467 " --> pdb=" O LYS H 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 76 removed outlier: 4.136A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.855A pdb=" N ASN D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 Processing helix chain 'D' and resid 114 through 131 removed outlier: 3.648A pdb=" N TYR D 118 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 144 removed outlier: 3.668A pdb=" N VAL D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 removed outlier: 4.085A pdb=" N LYS D 155 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 331 removed outlier: 3.542A pdb=" N MET D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 360 through 368 removed outlier: 3.918A pdb=" N GLU D 366 " --> pdb=" O ASN D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 399 removed outlier: 4.480A pdb=" N ASP D 395 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN D 398 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 424 removed outlier: 3.616A pdb=" N GLU D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 483 removed outlier: 3.884A pdb=" N ILE D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS D 434 " --> pdb=" O GLN D 430 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR D 452 " --> pdb=" O CYS D 448 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 476 " --> pdb=" O ARG D 472 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP D 481 " --> pdb=" O LYS D 477 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU D 482 " --> pdb=" O GLN D 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 47 removed outlier: 3.814A pdb=" N SER M 44 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY M 46 " --> pdb=" O LEU M 42 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL M 47 " --> pdb=" O GLN M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 70 removed outlier: 3.534A pdb=" N GLN M 69 " --> pdb=" O ASN M 66 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER M 70 " --> pdb=" O VAL M 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 66 through 70' Processing helix chain 'M' and resid 80 through 91 removed outlier: 3.548A pdb=" N LEU M 89 " --> pdb=" O MET M 85 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 90 " --> pdb=" O GLU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 111 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'M' and resid 123 through 132 removed outlier: 4.433A pdb=" N PHE M 130 " --> pdb=" O LEU M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 141 removed outlier: 4.162A pdb=" N ILE M 137 " --> pdb=" O PRO M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 168 removed outlier: 3.663A pdb=" N SER M 154 " --> pdb=" O LYS M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 181 Processing helix chain 'M' and resid 183 through 201 removed outlier: 3.551A pdb=" N GLY M 201 " --> pdb=" O CYS M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 210 No H-bonds generated for 'chain 'M' and resid 208 through 210' Processing helix chain 'M' and resid 211 through 230 removed outlier: 4.165A pdb=" N GLU M 217 " --> pdb=" O THR M 213 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU M 218 " --> pdb=" O PHE M 214 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR M 221 " --> pdb=" O GLU M 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU M 223 " --> pdb=" O THR M 219 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP M 224 " --> pdb=" O HIS M 220 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU M 225 " --> pdb=" O TYR M 221 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA M 228 " --> pdb=" O ASP M 224 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER M 230 " --> pdb=" O MET M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 233 No H-bonds generated for 'chain 'M' and resid 231 through 233' Processing helix chain 'M' and resid 240 through 250 removed outlier: 3.714A pdb=" N GLN M 244 " --> pdb=" O ASP M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 270 removed outlier: 3.741A pdb=" N LEU M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 278 through 282 Processing helix chain 'M' and resid 288 through 293 removed outlier: 3.609A pdb=" N VAL M 293 " --> pdb=" O LEU M 289 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 298 removed outlier: 3.512A pdb=" N LEU M 298 " --> pdb=" O PHE M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 317 Processing helix chain 'M' and resid 322 through 327 Processing helix chain 'M' and resid 331 through 340 removed outlier: 3.601A pdb=" N ILE M 335 " --> pdb=" O GLU M 331 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU M 336 " --> pdb=" O CYS M 332 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU M 337 " --> pdb=" O SER M 333 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA M 338 " --> pdb=" O LEU M 334 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU M 340 " --> pdb=" O LEU M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 524 through 538 removed outlier: 3.944A pdb=" N LYS M 528 " --> pdb=" O SER M 524 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 529 " --> pdb=" O ASP M 525 " (cutoff:3.500A) Processing helix chain 'M' and resid 545 through 551 Processing helix chain 'M' and resid 553 through 562 removed outlier: 4.282A pdb=" N HIS M 559 " --> pdb=" O PRO M 555 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS M 560 " --> pdb=" O LEU M 556 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA M 562 " --> pdb=" O LEU M 558 " (cutoff:3.500A) Processing helix chain 'M' and resid 565 through 570 removed outlier: 4.164A pdb=" N LEU M 569 " --> pdb=" O PRO M 565 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA M 570 " --> pdb=" O PRO M 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 565 through 570' Processing helix chain 'M' and resid 572 through 578 Processing helix chain 'I' and resid 29 through 54 Processing helix chain 'I' and resid 235 through 243 Processing helix chain 'I' and resid 249 through 263 Processing helix chain 'I' and resid 316 through 324 Processing helix chain 'I' and resid 331 through 342 removed outlier: 3.614A pdb=" N VAL I 339 " --> pdb=" O VAL I 335 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN I 340 " --> pdb=" O VAL I 336 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS I 341 " --> pdb=" O GLN I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 425 removed outlier: 3.728A pdb=" N PHE I 419 " --> pdb=" O LYS I 415 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 445 removed outlier: 4.333A pdb=" N HIS I 432 " --> pdb=" O GLU I 428 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS I 438 " --> pdb=" O LEU I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 473 through 478 removed outlier: 3.575A pdb=" N TYR I 478 " --> pdb=" O ILE I 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 161 through 168 Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 231 through 243 removed outlier: 3.509A pdb=" N LYS G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU G 243 " --> pdb=" O TYR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 264 Processing helix chain 'G' and resid 306 through 319 removed outlier: 3.567A pdb=" N ASP G 317 " --> pdb=" O SER G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 345 removed outlier: 3.892A pdb=" N LEU G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU G 334 " --> pdb=" O GLN G 330 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR G 335 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS G 341 " --> pdb=" O LEU G 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.828A pdb=" N VAL A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 17 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 75 through 82 removed outlier: 4.011A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 4.605A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 133 removed outlier: 3.578A pdb=" N GLN A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.819A pdb=" N TYR A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.516A pdb=" N ARG A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.947A pdb=" N ASN A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 3.951A pdb=" N ASN A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.527A pdb=" N SER A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 463 removed outlier: 4.037A pdb=" N LYS A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 14 removed outlier: 4.459A pdb=" N MET J 9 " --> pdb=" O GLN J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 24 removed outlier: 3.631A pdb=" N LEU J 23 " --> pdb=" O VAL J 20 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA J 24 " --> pdb=" O ALA J 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 20 through 24' Processing helix chain 'J' and resid 56 through 66 Processing helix chain 'J' and resid 75 through 101 removed outlier: 3.538A pdb=" N ILE J 79 " --> pdb=" O GLU J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 127 removed outlier: 4.256A pdb=" N LYS J 117 " --> pdb=" O ASP J 113 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS J 127 " --> pdb=" O GLN J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 197 removed outlier: 3.802A pdb=" N ILE J 193 " --> pdb=" O PRO J 189 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG J 194 " --> pdb=" O ASP J 190 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE J 195 " --> pdb=" O THR J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 207 Processing helix chain 'J' and resid 239 through 248 removed outlier: 3.673A pdb=" N GLU J 244 " --> pdb=" O LYS J 240 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 266 removed outlier: 3.524A pdb=" N GLN J 254 " --> pdb=" O LEU J 250 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER J 256 " --> pdb=" O THR J 252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS J 260 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN J 264 " --> pdb=" O LYS J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 290 removed outlier: 3.522A pdb=" N ALA J 283 " --> pdb=" O SER J 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN J 290 " --> pdb=" O GLN J 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 37 removed outlier: 3.677A pdb=" N ASN E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.523A pdb=" N HIS E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 72 Processing helix chain 'C' and resid 204 through 226 removed outlier: 3.861A pdb=" N ASN C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 176 removed outlier: 3.552A pdb=" N GLU K 176 " --> pdb=" O THR K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 173 through 176' Processing helix chain 'K' and resid 177 through 194 removed outlier: 4.165A pdb=" N GLU K 191 " --> pdb=" O GLY K 187 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 369 Processing helix chain 'X' and resid 381 through 390 removed outlier: 3.859A pdb=" N LYS X 385 " --> pdb=" O PRO X 381 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE X 388 " --> pdb=" O PHE X 384 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS X 390 " --> pdb=" O LYS X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 489 through 491 No H-bonds generated for 'chain 'X' and resid 489 through 491' Processing helix chain 'L' and resid 863 through 867 removed outlier: 3.860A pdb=" N GLY L 867 " --> pdb=" O PHE L 864 " (cutoff:3.500A) Processing helix chain 'L' and resid 871 through 883 removed outlier: 3.600A pdb=" N THR L 875 " --> pdb=" O SER L 871 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG L 883 " --> pdb=" O LEU L 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 359 through 360 Processing sheet with id=AA2, first strand: chain 'H' and resid 186 through 190 Processing sheet with id=AA3, first strand: chain 'H' and resid 80 through 83 removed outlier: 6.334A pdb=" N VAL H 80 " --> pdb=" O VAL D 190 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 192 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE H 82 " --> pdb=" O ASP D 192 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 270 through 274 Processing sheet with id=AA5, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA6, first strand: chain 'I' and resid 8 through 9 Processing sheet with id=AA7, first strand: chain 'I' and resid 219 through 222 removed outlier: 3.516A pdb=" N ILE I 222 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE I 349 " --> pdb=" O ILE I 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 233 through 234 Processing sheet with id=AA9, first strand: chain 'G' and resid 203 through 212 removed outlier: 3.717A pdb=" N HIS G 215 " --> pdb=" O HIS G 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 279 through 285 removed outlier: 3.521A pdb=" N GLU G 293 " --> pdb=" O ARG G 379 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 188 through 189 removed outlier: 3.618A pdb=" N VAL A 189 " --> pdb=" O GLN X 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 192 through 196 removed outlier: 4.253A pdb=" N SER A 192 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 228 " --> pdb=" O ALA X 497 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER X 499 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN A 230 " --> pdb=" O SER X 499 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N MET X 501 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE X 498 " --> pdb=" O TRP X 620 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN X 622 " --> pdb=" O PHE X 498 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE X 500 " --> pdb=" O ASN X 622 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG X 605 " --> pdb=" O LEU X 525 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU X 525 " --> pdb=" O ARG X 605 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 478 through 479 Processing sheet with id=AB5, first strand: chain 'C' and resid 198 through 200 Processing sheet with id=AB6, first strand: chain 'X' and resid 443 through 444 removed outlier: 3.537A pdb=" N SER X 513 " --> pdb=" O GLU X 589 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU X 589 " --> pdb=" O SER X 513 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 508 through 510 851 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6811 1.34 - 1.46: 3479 1.46 - 1.57: 11455 1.57 - 1.69: 0 1.69 - 1.81: 137 Bond restraints: 21882 Sorted by residual: bond pdb=" C ILE G 325 " pdb=" N PRO G 326 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.20e-02 6.94e+03 1.57e+01 bond pdb=" N GLU X 439 " pdb=" CA GLU X 439 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 bond pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.27e-02 6.20e+03 7.49e+00 bond pdb=" N GLN X 440 " pdb=" CA GLN X 440 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.45e+00 bond pdb=" N THR A 235 " pdb=" CA THR A 235 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.26e+00 ... (remaining 21877 not shown) Histogram of bond angle deviations from ideal: 96.23 - 103.80: 292 103.80 - 111.38: 8747 111.38 - 118.95: 9064 118.95 - 126.52: 11190 126.52 - 134.10: 290 Bond angle restraints: 29583 Sorted by residual: angle pdb=" N PRO J 17 " pdb=" CA PRO J 17 " pdb=" CB PRO J 17 " ideal model delta sigma weight residual 103.25 110.26 -7.01 1.05e+00 9.07e-01 4.45e+01 angle pdb=" N LYS G 338 " pdb=" CA LYS G 338 " pdb=" C LYS G 338 " ideal model delta sigma weight residual 112.04 102.54 9.50 1.44e+00 4.82e-01 4.35e+01 angle pdb=" N ILE M 553 " pdb=" CA ILE M 553 " pdb=" C ILE M 553 " ideal model delta sigma weight residual 113.53 107.52 6.01 9.80e-01 1.04e+00 3.76e+01 angle pdb=" C HIS H 261 " pdb=" N THR H 262 " pdb=" CA THR H 262 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" N LYS G 340 " pdb=" CA LYS G 340 " pdb=" C LYS G 340 " ideal model delta sigma weight residual 111.28 105.88 5.40 1.09e+00 8.42e-01 2.45e+01 ... (remaining 29578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 12742 15.98 - 31.95: 531 31.95 - 47.93: 137 47.93 - 63.90: 8 63.90 - 79.88: 13 Dihedral angle restraints: 13431 sinusoidal: 5563 harmonic: 7868 Sorted by residual: dihedral pdb=" CA THR H 452 " pdb=" C THR H 452 " pdb=" N GLN H 453 " pdb=" CA GLN H 453 " ideal model delta harmonic sigma weight residual -180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA GLU H 464 " pdb=" C GLU H 464 " pdb=" N SER H 465 " pdb=" CA SER H 465 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER G 275 " pdb=" C SER G 275 " pdb=" N ASP G 276 " pdb=" CA ASP G 276 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 13428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2607 0.060 - 0.119: 661 0.119 - 0.179: 93 0.179 - 0.239: 15 0.239 - 0.298: 5 Chirality restraints: 3381 Sorted by residual: chirality pdb=" CA ILE A 237 " pdb=" N ILE A 237 " pdb=" C ILE A 237 " pdb=" CB ILE A 237 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE M 115 " pdb=" CA ILE M 115 " pdb=" CG1 ILE M 115 " pdb=" CG2 ILE M 115 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO J 17 " pdb=" N PRO J 17 " pdb=" C PRO J 17 " pdb=" CB PRO J 17 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3378 not shown) Planarity restraints: 3775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 256 " -0.063 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO A 257 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 270 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 271 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 862 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO L 863 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 863 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 863 " -0.040 5.00e-02 4.00e+02 ... (remaining 3772 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 11 2.29 - 2.94: 8647 2.94 - 3.60: 29652 3.60 - 4.25: 45812 4.25 - 4.90: 76680 Nonbonded interactions: 160802 Sorted by model distance: nonbonded pdb=" OE1 GLU X 439 " pdb=" CG GLU X 490 " model vdw 1.639 3.440 nonbonded pdb=" OE2 GLU A 238 " pdb=" ND2 ASN J 212 " model vdw 1.706 2.520 nonbonded pdb=" OE1 GLU X 439 " pdb=" CD GLU X 490 " model vdw 2.087 3.270 nonbonded pdb=" CD GLU A 238 " pdb=" ND2 ASN J 212 " model vdw 2.182 3.350 nonbonded pdb=" OG SER D 316 " pdb=" OE1 GLU D 319 " model vdw 2.225 2.440 ... (remaining 160797 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.540 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 58.480 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.005 0.071 21882 Z= 0.317 Angle : 0.959 12.252 29583 Z= 0.531 Chirality : 0.054 0.298 3381 Planarity : 0.007 0.096 3775 Dihedral : 10.227 79.881 8277 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 0.33 % Allowed : 3.17 % Favored : 96.50 % 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: -4.21 (0.13), residues: 2581 helix: -2.49 (0.11), residues: 1286 sheet: -3.31 (0.34), residues: 150 loop : -3.00 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 371 HIS 0.013 0.002 HIS A 270 PHE 0.034 0.002 PHE J 83 TYR 0.026 0.002 TYR F 410 ARG 0.013 0.001 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 658 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 665 average time/residue: 0.3860 time to fit residues: 377.6367 Evaluate side-chains 298 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 296 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2045 time to fit residues: 4.8385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.7980 chunk 196 optimal weight: 0.5980 chunk 108 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 ASN H 167 ASN H 186 HIS H 195 GLN H 239 GLN H 250 ASN H 281 ASN H 314 ASN H 318 GLN H 470 ASN D 145 ASN D 167 ASN M 359 HIS I 245 GLN I 432 HIS I 463 ASN I 464 ASN I 465 ASN G 158 GLN G 352 HIS A 112 GLN ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN J 123 GLN J 259 GLN J 263 ASN E 23 ASN K 160 GLN K 174 GLN X 380 ASN X 493 GLN X 494 ASN X 600 ASN L 800 ASN L 810 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21882 Z= 0.169 Angle : 0.612 10.027 29583 Z= 0.316 Chirality : 0.042 0.239 3381 Planarity : 0.005 0.072 3775 Dihedral : 5.298 22.649 2835 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.10 % Allowed : 10.57 % Favored : 87.33 % 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: -2.54 (0.15), residues: 2581 helix: -0.71 (0.14), residues: 1291 sheet: -2.92 (0.35), residues: 147 loop : -2.67 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 334 HIS 0.006 0.001 HIS A 270 PHE 0.017 0.001 PHE L 864 TYR 0.026 0.001 TYR X 368 ARG 0.010 0.001 ARG L 764 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 355 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 391 average time/residue: 0.3329 time to fit residues: 201.5029 Evaluate side-chains 292 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 2.397 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1952 time to fit residues: 13.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 254 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 364 GLN ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 ASN H 265 ASN D 127 ASN ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS A 392 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN J 254 GLN J 259 GLN J 271 HIS E 23 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 21882 Z= 0.352 Angle : 0.688 16.417 29583 Z= 0.351 Chirality : 0.045 0.161 3381 Planarity : 0.005 0.069 3775 Dihedral : 5.267 22.506 2835 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.39 % Allowed : 12.59 % Favored : 85.03 % 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: -1.85 (0.16), residues: 2581 helix: -0.03 (0.14), residues: 1296 sheet: -2.65 (0.37), residues: 140 loop : -2.51 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 791 HIS 0.008 0.001 HIS F 358 PHE 0.019 0.002 PHE G 359 TYR 0.033 0.002 TYR H 272 ARG 0.006 0.001 ARG M 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 277 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 33 residues processed: 321 average time/residue: 0.3304 time to fit residues: 165.4875 Evaluate side-chains 281 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 248 time to evaluate : 2.491 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1880 time to fit residues: 14.9621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 0.0270 chunk 158 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 250 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN D 145 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 480 GLN G 220 GLN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN A 392 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21882 Z= 0.178 Angle : 0.575 9.060 29583 Z= 0.293 Chirality : 0.041 0.162 3381 Planarity : 0.004 0.066 3775 Dihedral : 4.798 21.734 2835 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.44 % Allowed : 14.27 % Favored : 84.29 % 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: -1.27 (0.17), residues: 2581 helix: 0.59 (0.15), residues: 1268 sheet: -2.46 (0.39), residues: 130 loop : -2.33 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 481 HIS 0.007 0.001 HIS A 270 PHE 0.013 0.001 PHE A 450 TYR 0.020 0.001 TYR G 361 ARG 0.006 0.000 ARG I 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 281 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 16 residues processed: 306 average time/residue: 0.3566 time to fit residues: 168.4338 Evaluate side-chains 257 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 241 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2353 time to fit residues: 10.2363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 0.0370 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 425 GLN ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 233 ASN H 470 ASN D 102 ASN D 145 ASN ** I 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 334 ASN ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 HIS A 392 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 GLN ** X 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21882 Z= 0.229 Angle : 0.593 12.836 29583 Z= 0.300 Chirality : 0.042 0.169 3381 Planarity : 0.004 0.061 3775 Dihedral : 4.699 26.182 2835 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.65 % Allowed : 15.34 % Favored : 83.01 % 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: -1.05 (0.17), residues: 2581 helix: 0.77 (0.15), residues: 1277 sheet: -2.27 (0.38), residues: 144 loop : -2.25 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 791 HIS 0.010 0.001 HIS L 877 PHE 0.023 0.001 PHE G 359 TYR 0.022 0.002 TYR D 168 ARG 0.006 0.000 ARG I 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 253 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 280 average time/residue: 0.3362 time to fit residues: 146.8502 Evaluate side-chains 254 residues out of total 2458 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 235 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2037 time to fit residues: 10.4739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 53.7795 > 50: distance: 55 - 60: 8.617 distance: 60 - 61: 4.550 distance: 61 - 62: 3.349 distance: 61 - 64: 6.587 distance: 62 - 63: 9.433 distance: 62 - 68: 6.590 distance: 65 - 67: 5.282 distance: 68 - 69: 11.227 distance: 68 - 74: 6.534 distance: 69 - 70: 14.140 distance: 69 - 72: 7.959 distance: 70 - 71: 10.344 distance: 70 - 75: 14.503 distance: 71 - 99: 9.996 distance: 72 - 73: 11.177 distance: 73 - 74: 8.404 distance: 75 - 76: 6.865 distance: 76 - 77: 10.993 distance: 76 - 79: 25.421 distance: 77 - 78: 10.787 distance: 77 - 83: 14.511 distance: 78 - 106: 28.396 distance: 79 - 80: 3.571 distance: 80 - 81: 11.800 distance: 80 - 82: 17.892 distance: 83 - 84: 11.941 distance: 84 - 85: 22.454 distance: 84 - 87: 3.970 distance: 85 - 86: 25.078 distance: 85 - 91: 18.620 distance: 86 - 113: 13.408 distance: 87 - 88: 23.084 distance: 88 - 89: 28.408 distance: 89 - 90: 14.644 distance: 91 - 92: 23.260 distance: 92 - 93: 19.550 distance: 92 - 95: 40.257 distance: 93 - 94: 8.111 distance: 93 - 99: 7.306 distance: 94 - 122: 23.005 distance: 95 - 96: 18.149 distance: 96 - 97: 11.834 distance: 96 - 98: 22.035 distance: 99 - 100: 17.230 distance: 100 - 101: 13.210 distance: 100 - 103: 5.405 distance: 101 - 102: 17.100 distance: 101 - 106: 13.949 distance: 103 - 104: 14.036 distance: 103 - 105: 14.372 distance: 106 - 107: 14.519 distance: 107 - 108: 5.892 distance: 107 - 110: 16.447 distance: 108 - 109: 15.243 distance: 108 - 113: 6.405 distance: 110 - 111: 18.856 distance: 110 - 112: 24.587 distance: 113 - 114: 3.199 distance: 114 - 115: 6.398 distance: 114 - 117: 10.268 distance: 115 - 116: 4.694 distance: 115 - 122: 4.411 distance: 117 - 118: 8.808 distance: 118 - 119: 9.417 distance: 119 - 120: 10.096 distance: 119 - 121: 7.381 distance: 122 - 123: 9.215 distance: 123 - 124: 3.500 distance: 123 - 126: 16.263 distance: 124 - 125: 4.245 distance: 124 - 129: 6.457 distance: 125 - 149: 8.027 distance: 126 - 127: 18.126 distance: 126 - 128: 5.616 distance: 129 - 130: 11.600 distance: 130 - 131: 7.660 distance: 130 - 133: 15.696 distance: 131 - 132: 16.455 distance: 131 - 136: 9.874 distance: 133 - 134: 11.567 distance: 133 - 135: 5.716