Starting phenix.real_space_refine on Sat Jun 29 07:57:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjk_33873/06_2024/7yjk_33873_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjk_33873/06_2024/7yjk_33873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjk_33873/06_2024/7yjk_33873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjk_33873/06_2024/7yjk_33873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjk_33873/06_2024/7yjk_33873_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjk_33873/06_2024/7yjk_33873_updated.pdb" } resolution = 3.2 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= 0.006 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 P 2 5.49 5 S 100 5.16 5 C 11390 2.51 5 N 2978 2.21 5 O 3188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 54": "NH1" <-> "NH2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ASP 308": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "D TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ASP 194": "OD1" <-> "OD2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 277": "NH1" <-> "NH2" Residue "E ARG 294": "NH1" <-> "NH2" Residue "E ASP 308": "OD1" <-> "OD2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 330": "NH1" <-> "NH2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 396": "NH1" <-> "NH2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E ARG 425": "NH1" <-> "NH2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E ARG 439": "NH1" <-> "NH2" Residue "E ASP 443": "OD1" <-> "OD2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "E ARG 473": "NH1" <-> "NH2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 58": "NH1" <-> "NH2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 65": "OD1" <-> "OD2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 234": "NH1" <-> "NH2" Residue "F TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 298": "OD1" <-> "OD2" Residue "F ASP 301": "OD1" <-> "OD2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F ARG 375": "NH1" <-> "NH2" Residue "F PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 382": "NH1" <-> "NH2" Residue "F ASP 397": "OD1" <-> "OD2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "F ARG 420": "NH1" <-> "NH2" Residue "F ARG 450": "NH1" <-> "NH2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F ASP 452": "OD1" <-> "OD2" Residue "F ARG 455": "NH1" <-> "NH2" Residue "F PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 475": "OE1" <-> "OE2" Residue "H TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 6": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 17658 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 424} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3665 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 21, 'TRANS': 448} Chain breaks: 1 Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 402 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 424} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3665 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 21, 'TRANS': 448} Chain breaks: 1 Chain: "H" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "G" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 402 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 8.16, per 1000 atoms: 0.46 Number of scatterers: 17658 At special positions: 0 Unit cell: (126.36, 145.8, 118.8, 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) S 100 16.00 P 2 15.00 O 3188 8.00 N 2978 7.00 C 11390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.82 Conformation dependent library (CDL) restraints added in 2.9 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 8 sheets defined 42.3% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.887A pdb=" N GLY A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 128 through 136 removed outlier: 3.598A pdb=" N THR A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.653A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 189' Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.528A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.534A pdb=" N LYS A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.713A pdb=" N GLU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.716A pdb=" N ALA A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 383 removed outlier: 3.585A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.763A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.715A pdb=" N SER A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 29 removed outlier: 3.649A pdb=" N SER B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.834A pdb=" N GLN B 64 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.738A pdb=" N GLU B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 217 through 230 removed outlier: 3.852A pdb=" N ARG B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 268 removed outlier: 4.016A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 294 No H-bonds generated for 'chain 'B' and resid 291 through 294' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.569A pdb=" N HIS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.619A pdb=" N GLN B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 387 removed outlier: 3.839A pdb=" N LYS B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 420 Proline residue: B 412 - end of helix removed outlier: 3.516A pdb=" N SER B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 418 " --> pdb=" O PHE B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 removed outlier: 3.599A pdb=" N LYS B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 26 through 44 removed outlier: 3.511A pdb=" N LEU D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 42 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 68 removed outlier: 3.664A pdb=" N VAL D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'D' and resid 88 through 95 removed outlier: 3.505A pdb=" N MET D 92 " --> pdb=" O TRP D 88 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP D 93 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASN D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 95' Processing helix chain 'D' and resid 100 through 118 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 127 through 140 Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.557A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 45 removed outlier: 3.563A pdb=" N LEU C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 45 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 53 removed outlier: 3.886A pdb=" N GLY E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 128 through 136 removed outlier: 3.598A pdb=" N THR E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 167 Processing helix chain 'E' and resid 178 through 181 Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.653A pdb=" N PHE E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'E' and resid 204 through 212 removed outlier: 3.527A pdb=" N GLY E 209 " --> pdb=" O GLY E 205 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 238 removed outlier: 3.534A pdb=" N LYS E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 274 removed outlier: 3.713A pdb=" N GLU E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 329 through 335 Processing helix chain 'E' and resid 350 through 365 removed outlier: 3.716A pdb=" N ALA E 355 " --> pdb=" O TYR E 351 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE E 357 " --> pdb=" O ALA E 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR E 358 " --> pdb=" O SER E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 383 removed outlier: 3.586A pdb=" N LEU E 373 " --> pdb=" O MET E 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN E 376 " --> pdb=" O LYS E 372 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 383 " --> pdb=" O LEU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 428 removed outlier: 3.763A pdb=" N LEU E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 476 removed outlier: 3.716A pdb=" N SER E 468 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 29 removed outlier: 3.649A pdb=" N SER F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 57 No H-bonds generated for 'chain 'F' and resid 54 through 57' Processing helix chain 'F' and resid 61 through 66 removed outlier: 3.835A pdb=" N GLN F 64 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP F 65 " --> pdb=" O ARG F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.738A pdb=" N GLU F 152 " --> pdb=" O HIS F 148 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 178 through 181 No H-bonds generated for 'chain 'F' and resid 178 through 181' Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 217 through 230 removed outlier: 3.852A pdb=" N ARG F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 226 " --> pdb=" O ARG F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 268 removed outlier: 4.015A pdb=" N ILE F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 294 No H-bonds generated for 'chain 'F' and resid 291 through 294' Processing helix chain 'F' and resid 324 through 333 removed outlier: 3.568A pdb=" N HIS F 332 " --> pdb=" O GLN F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 338 No H-bonds generated for 'chain 'F' and resid 335 through 338' Processing helix chain 'F' and resid 346 through 359 removed outlier: 3.620A pdb=" N GLN F 350 " --> pdb=" O PRO F 346 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE F 351 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 354 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 387 removed outlier: 3.839A pdb=" N LYS F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE F 380 " --> pdb=" O GLU F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 420 Proline residue: F 412 - end of helix removed outlier: 3.517A pdb=" N SER F 415 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 417 " --> pdb=" O ALA F 413 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS F 418 " --> pdb=" O PHE F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 466 removed outlier: 3.600A pdb=" N LYS F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP F 465 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 18 No H-bonds generated for 'chain 'H' and resid 16 through 18' Processing helix chain 'H' and resid 20 through 22 No H-bonds generated for 'chain 'H' and resid 20 through 22' Processing helix chain 'H' and resid 26 through 44 removed outlier: 3.511A pdb=" N LEU H 34 " --> pdb=" O TYR H 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU H 42 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 68 removed outlier: 3.664A pdb=" N VAL H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 88 through 95 removed outlier: 3.506A pdb=" N MET H 92 " --> pdb=" O TRP H 88 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP H 93 " --> pdb=" O TRP H 89 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ASN H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY H 95 " --> pdb=" O GLN H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 95' Processing helix chain 'H' and resid 100 through 118 Proline residue: H 109 - end of helix Processing helix chain 'H' and resid 127 through 140 Processing helix chain 'G' and resid 3 through 14 removed outlier: 3.557A pdb=" N THR G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 45 removed outlier: 3.563A pdb=" N LEU G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG G 45 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.525A pdb=" N THR A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 111 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.643A pdb=" N ASP A 171 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 327 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 281 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 195 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 250 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 197 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLU A 252 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR A 216 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.829A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR B 319 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 308 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 187 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL B 245 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 189 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR B 208 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG B 210 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.680A pdb=" N ILE B 442 " --> pdb=" O MET B 401 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 439 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 426 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 103 through 106 removed outlier: 3.525A pdb=" N THR E 104 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 111 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 171 through 175 removed outlier: 3.643A pdb=" N ASP E 171 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY E 327 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP E 281 " --> pdb=" O ALA E 251 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL E 195 " --> pdb=" O TYR E 248 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL E 250 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 197 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLU E 252 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR E 216 " --> pdb=" O ILE E 196 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 163 through 167 removed outlier: 3.829A pdb=" N GLY F 318 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR F 319 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR F 308 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 187 " --> pdb=" O ILE F 243 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL F 245 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE F 189 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR F 208 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER F 190 " --> pdb=" O THR F 208 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG F 210 " --> pdb=" O SER F 190 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 400 through 404 removed outlier: 3.679A pdb=" N ILE F 442 " --> pdb=" O MET F 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG F 439 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 426 " --> pdb=" O ARG F 441 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 6.48 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: 5575 1.34 - 1.46: 3163 1.46 - 1.57: 9172 1.57 - 1.69: 4 1.69 - 1.81: 156 Bond restraints: 18070 Sorted by residual: bond pdb=" C ARG E 62 " pdb=" N PRO E 63 " ideal model delta sigma weight residual 1.332 1.589 -0.258 1.26e-02 6.30e+03 4.18e+02 bond pdb=" C ARG A 62 " pdb=" N PRO A 63 " ideal model delta sigma weight residual 1.332 1.589 -0.258 1.26e-02 6.30e+03 4.18e+02 bond pdb=" C14 Z1T F 502 " pdb=" C15 Z1T F 502 " ideal model delta sigma weight residual 1.329 1.525 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C14 Z1T B 502 " pdb=" C15 Z1T B 502 " ideal model delta sigma weight residual 1.329 1.525 -0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" C13 Z1T B 502 " pdb=" C14 Z1T B 502 " ideal model delta sigma weight residual 1.494 1.525 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 18065 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.59: 519 106.59 - 113.46: 9975 113.46 - 120.33: 6986 120.33 - 127.21: 6787 127.21 - 134.08: 207 Bond angle restraints: 24474 Sorted by residual: angle pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" C ARG B 30 " ideal model delta sigma weight residual 113.55 106.70 6.85 1.26e+00 6.30e-01 2.95e+01 angle pdb=" N ARG F 30 " pdb=" CA ARG F 30 " pdb=" C ARG F 30 " ideal model delta sigma weight residual 113.55 106.71 6.84 1.26e+00 6.30e-01 2.95e+01 angle pdb=" N GLU F 253 " pdb=" CA GLU F 253 " pdb=" C GLU F 253 " ideal model delta sigma weight residual 114.75 108.80 5.95 1.26e+00 6.30e-01 2.23e+01 angle pdb=" N GLU B 253 " pdb=" CA GLU B 253 " pdb=" C GLU B 253 " ideal model delta sigma weight residual 114.75 108.85 5.90 1.26e+00 6.30e-01 2.19e+01 angle pdb=" C SER F 398 " pdb=" N PRO F 399 " pdb=" CA PRO F 399 " ideal model delta sigma weight residual 119.56 123.65 -4.09 1.01e+00 9.80e-01 1.64e+01 ... (remaining 24469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 9619 17.41 - 34.81: 906 34.81 - 52.22: 188 52.22 - 69.63: 32 69.63 - 87.04: 17 Dihedral angle restraints: 10762 sinusoidal: 4304 harmonic: 6458 Sorted by residual: dihedral pdb=" CA VAL E 288 " pdb=" C VAL E 288 " pdb=" N LEU E 289 " pdb=" CA LEU E 289 " ideal model delta harmonic sigma weight residual 180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL A 288 " pdb=" C VAL A 288 " pdb=" N LEU A 289 " pdb=" CA LEU A 289 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY F 50 " pdb=" C GLY F 50 " pdb=" N HIS F 51 " pdb=" CA HIS F 51 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1841 0.050 - 0.100: 737 0.100 - 0.150: 154 0.150 - 0.200: 6 0.200 - 0.251: 2 Chirality restraints: 2740 Sorted by residual: chirality pdb=" CA TYR D 122 " pdb=" N TYR D 122 " pdb=" C TYR D 122 " pdb=" CB TYR D 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA TYR H 122 " pdb=" N TYR H 122 " pdb=" C TYR H 122 " pdb=" CB TYR H 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA GLU A 477 " pdb=" N GLU A 477 " pdb=" C GLU A 477 " pdb=" CB GLU A 477 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 2737 not shown) Planarity restraints: 3074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 433 " 0.053 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO F 434 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 434 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 434 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 433 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO B 434 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.72e+00 pdb=" N PRO A 60 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.038 5.00e-02 4.00e+02 ... (remaining 3071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3142 2.76 - 3.29: 16171 3.29 - 3.83: 26638 3.83 - 4.36: 32636 4.36 - 4.90: 58129 Nonbonded interactions: 136716 Sorted by model distance: nonbonded pdb=" O LEU A 43 " pdb=" CG2 VAL A 46 " model vdw 2.223 3.460 nonbonded pdb=" O LEU E 43 " pdb=" CG2 VAL E 46 " model vdw 2.223 3.460 nonbonded pdb=" ND1 HIS D 118 " pdb=" OE2 GLU E 41 " model vdw 2.234 2.520 nonbonded pdb=" OE2 GLU A 41 " pdb=" ND1 HIS H 118 " model vdw 2.239 2.520 nonbonded pdb=" OD2 ASP F 27 " pdb=" NH2 ARG F 57 " model vdw 2.245 2.520 ... (remaining 136711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 43.630 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.008 0.258 18070 Z= 0.535 Angle : 0.892 10.604 24474 Z= 0.535 Chirality : 0.053 0.251 2740 Planarity : 0.006 0.079 3074 Dihedral : 14.225 87.037 6622 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.13 % Favored : 92.15 % Rotamer: Outliers : 0.21 % Allowed : 1.05 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.17), residues: 2216 helix: -1.76 (0.15), residues: 1046 sheet: -1.60 (0.33), residues: 238 loop : -2.40 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 23 HIS 0.008 0.001 HIS F 337 PHE 0.024 0.002 PHE E 220 TYR 0.033 0.002 TYR E 177 ARG 0.005 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 1.971 Fit side-chains REVERT: A 52 LEU cc_start: 0.8478 (tt) cc_final: 0.8136 (mp) REVERT: A 246 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7897 (mtt180) REVERT: B 28 PHE cc_start: 0.7619 (t80) cc_final: 0.7349 (t80) REVERT: B 30 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7299 (mpt180) REVERT: D 1 MET cc_start: 0.4792 (ttm) cc_final: 0.4160 (ptm) REVERT: E 52 LEU cc_start: 0.8461 (tt) cc_final: 0.8116 (mp) REVERT: E 246 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7892 (mtt180) REVERT: F 28 PHE cc_start: 0.7590 (t80) cc_final: 0.7232 (t80) REVERT: F 30 ARG cc_start: 0.7797 (tpt170) cc_final: 0.7250 (mpt180) REVERT: H 1 MET cc_start: 0.4822 (ttm) cc_final: 0.4140 (ptm) outliers start: 4 outliers final: 4 residues processed: 211 average time/residue: 0.3071 time to fit residues: 96.3001 Evaluate side-chains 183 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 428 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 HIS ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN E 223 ASN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18070 Z= 0.142 Angle : 0.536 8.195 24474 Z= 0.277 Chirality : 0.042 0.144 2740 Planarity : 0.005 0.077 3074 Dihedral : 6.855 59.408 2536 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 0.68 % Allowed : 6.41 % Favored : 92.91 % 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 (0.18), residues: 2216 helix: -0.54 (0.17), residues: 1008 sheet: -0.99 (0.35), residues: 252 loop : -1.99 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 23 HIS 0.005 0.001 HIS E 37 PHE 0.019 0.001 PHE B 79 TYR 0.011 0.001 TYR E 177 ARG 0.002 0.000 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 2.054 Fit side-chains REVERT: A 246 ARG cc_start: 0.8188 (mtm180) cc_final: 0.7776 (mtt180) REVERT: B 30 ARG cc_start: 0.7827 (tpt170) cc_final: 0.7312 (mpt180) REVERT: B 171 TYR cc_start: 0.7540 (t80) cc_final: 0.7217 (t80) REVERT: C 32 VAL cc_start: 0.8557 (p) cc_final: 0.8344 (p) REVERT: E 421 LYS cc_start: 0.8699 (ptmt) cc_final: 0.8186 (ptmm) REVERT: F 30 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7320 (mpt180) REVERT: F 171 TYR cc_start: 0.7610 (t80) cc_final: 0.7269 (t80) outliers start: 13 outliers final: 8 residues processed: 194 average time/residue: 0.3139 time to fit residues: 91.5447 Evaluate side-chains 168 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 160 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN D 96 GLN E 207 GLN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN H 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 18070 Z= 0.470 Angle : 0.680 7.678 24474 Z= 0.352 Chirality : 0.050 0.165 2740 Planarity : 0.006 0.079 3074 Dihedral : 6.553 58.010 2524 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.31 % Favored : 92.33 % Rotamer: Outliers : 2.31 % Allowed : 9.77 % Favored : 87.92 % 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: -2.02 (0.18), residues: 2216 helix: -0.64 (0.16), residues: 1002 sheet: -1.15 (0.32), residues: 284 loop : -2.11 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 23 HIS 0.007 0.002 HIS E 203 PHE 0.036 0.002 PHE B 79 TYR 0.017 0.002 TYR F 110 ARG 0.005 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.873 Fit side-chains REVERT: B 30 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7491 (mpt180) REVERT: D 96 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7651 (tt0) REVERT: F 30 ARG cc_start: 0.8042 (tpt170) cc_final: 0.7486 (mpt180) REVERT: H 96 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7640 (tt0) outliers start: 44 outliers final: 30 residues processed: 199 average time/residue: 0.2733 time to fit residues: 84.8164 Evaluate side-chains 192 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 414 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 463 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.786 > 50: distance: 27 - 140: 22.973 distance: 45 - 143: 24.676 distance: 48 - 158: 24.529 distance: 60 - 161: 17.031 distance: 114 - 118: 12.842 distance: 118 - 119: 13.047 distance: 119 - 120: 40.850 distance: 119 - 122: 27.233 distance: 120 - 121: 19.118 distance: 120 - 129: 17.535 distance: 122 - 123: 25.947 distance: 123 - 124: 31.742 distance: 124 - 125: 6.080 distance: 125 - 126: 14.697 distance: 126 - 127: 18.492 distance: 126 - 128: 17.861 distance: 129 - 130: 26.897 distance: 130 - 131: 29.454 distance: 130 - 133: 12.897 distance: 131 - 132: 41.049 distance: 131 - 140: 33.710 distance: 133 - 134: 10.567 distance: 134 - 135: 11.065 distance: 134 - 136: 13.149 distance: 135 - 137: 7.008 distance: 136 - 138: 19.918 distance: 137 - 139: 9.314 distance: 138 - 139: 10.715 distance: 140 - 141: 35.204 distance: 141 - 142: 31.812 distance: 141 - 144: 18.665 distance: 142 - 143: 40.353 distance: 142 - 151: 51.916 distance: 144 - 145: 5.757 distance: 145 - 146: 12.842 distance: 146 - 147: 13.102 distance: 147 - 148: 10.654 distance: 148 - 149: 20.238 distance: 148 - 150: 19.766 distance: 151 - 152: 29.268 distance: 152 - 153: 43.339 distance: 152 - 155: 15.956 distance: 153 - 154: 7.297 distance: 153 - 158: 34.043 distance: 154 - 240: 27.181 distance: 155 - 156: 6.745 distance: 155 - 157: 23.184 distance: 158 - 159: 49.544 distance: 159 - 160: 35.208 distance: 159 - 162: 48.118 distance: 160 - 161: 39.564 distance: 160 - 166: 40.140 distance: 162 - 163: 37.518 distance: 162 - 164: 50.972 distance: 163 - 165: 24.540 distance: 166 - 167: 26.767 distance: 166 - 243: 26.704 distance: 167 - 168: 40.642 distance: 167 - 170: 17.241 distance: 168 - 169: 44.589 distance: 168 - 174: 47.825 distance: 169 - 254: 22.051 distance: 171 - 172: 23.929 distance: 171 - 173: 25.013 distance: 174 - 175: 57.725 distance: 175 - 176: 47.425 distance: 175 - 178: 21.059 distance: 176 - 177: 23.327 distance: 176 - 182: 18.583 distance: 178 - 179: 35.697 distance: 179 - 180: 57.089 distance: 182 - 183: 24.588 distance: 183 - 184: 27.673 distance: 183 - 186: 30.003 distance: 184 - 185: 17.801 distance: 184 - 191: 18.524 distance: 186 - 187: 19.290 distance: 187 - 188: 5.096 distance: 188 - 189: 31.072 distance: 188 - 190: 22.803 distance: 191 - 192: 9.580 distance: 192 - 193: 21.065 distance: 192 - 195: 17.668 distance: 193 - 194: 13.908 distance: 193 - 197: 8.989 distance: 195 - 196: 18.737 distance: 197 - 198: 10.600 distance: 198 - 199: 24.836 distance: 198 - 201: 11.889 distance: 199 - 200: 6.862 distance: 199 - 205: 26.277 distance: 201 - 202: 31.545 distance: 202 - 203: 12.676 distance: 202 - 204: 19.410