Starting phenix.real_space_refine on Fri Dec 15 16:55:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/12_2023/6pp6_20420_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/12_2023/6pp6_20420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/12_2023/6pp6_20420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/12_2023/6pp6_20420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/12_2023/6pp6_20420_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pp6_20420/12_2023/6pp6_20420_trim_updated.pdb" } resolution = 4.28 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 S 35 5.16 5 C 10050 2.51 5 N 2691 2.21 5 O 3187 1.98 5 H 16126 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ASP 194": "OD1" <-> "OD2" Residue "C ASP 201": "OD1" <-> "OD2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 392": "OD1" <-> "OD2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 103": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ARG 200": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 279": "OD1" <-> "OD2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 382": "OD1" <-> "OD2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 279": "OD1" <-> "OD2" Residue "F ASP 294": "OD1" <-> "OD2" Residue "F PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 392": "OD1" <-> "OD2" Residue "F TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 32106 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5330 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain breaks: 2 Chain: "B" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "C" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5353 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 13, 'TRANS': 332} Chain breaks: 1 Chain: "D" Number of atoms: 5380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5380 Classifications: {'peptide': 349} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 1 Chain: "E" Number of atoms: 5336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 5336 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 Chain: "F" Number of atoms: 5125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 5125 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.39, per 1000 atoms: 0.45 Number of scatterers: 32106 At special positions: 0 Unit cell: (147.32, 140.36, 104.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 17 15.00 O 3187 8.00 N 2691 7.00 C 10050 6.00 H 16126 1.00 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: 27.33 Conformation dependent library (CDL) restraints added in 3.7 seconds 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 15 sheets defined 44.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 67 through 77 removed outlier: 3.813A pdb=" N TYR A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.585A pdb=" N LYS A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.549A pdb=" N ALA A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.671A pdb=" N LYS A 164 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.711A pdb=" N LYS A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'A' and resid 352 through 365 Processing helix chain 'A' and resid 369 through 379 removed outlier: 4.173A pdb=" N ARG A 373 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 377 " --> pdb=" O SER A 374 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.719A pdb=" N ASP A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.810A pdb=" N ASP B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 98 removed outlier: 3.886A pdb=" N VAL B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.570A pdb=" N ALA B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.529A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 168 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.572A pdb=" N LEU B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 292 through 298 removed outlier: 3.655A pdb=" N ILE B 296 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 298' Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.612A pdb=" N LYS B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.903A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 removed outlier: 3.727A pdb=" N ALA B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.502A pdb=" N ALA B 378 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.675A pdb=" N ASP B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'C' and resid 67 through 76 removed outlier: 3.685A pdb=" N ASP C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.502A pdb=" N LYS C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS C 97 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.704A pdb=" N ALA C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 205 through 216 removed outlier: 4.477A pdb=" N LYS C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.597A pdb=" N ARG C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 292 through 298 removed outlier: 3.770A pdb=" N LYS C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 removed outlier: 3.823A pdb=" N ARG C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 3.530A pdb=" N ILE C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN C 324 " --> pdb=" O GLU C 320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 removed outlier: 4.006A pdb=" N GLU C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 365 removed outlier: 3.834A pdb=" N ALA C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 387 removed outlier: 3.504A pdb=" N GLU C 377 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 378 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 383 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET C 384 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 387 " --> pdb=" O MET C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 404 removed outlier: 3.602A pdb=" N ASP C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 400 through 404' Processing helix chain 'D' and resid 67 through 76 Processing helix chain 'D' and resid 82 through 100 removed outlier: 3.983A pdb=" N VAL D 87 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS D 97 " --> pdb=" O TYR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.617A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 173 through 176 No H-bonds generated for 'chain 'D' and resid 173 through 176' Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.490A pdb=" N LYS D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 3.521A pdb=" N HIS D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 292 through 298 removed outlier: 3.951A pdb=" N LYS D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 Processing helix chain 'D' and resid 319 through 327 removed outlier: 3.703A pdb=" N ILE D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.623A pdb=" N GLU D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 365 removed outlier: 3.505A pdb=" N ASP D 356 " --> pdb=" O ASP D 352 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 364 " --> pdb=" O LYS D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 387 removed outlier: 3.764A pdb=" N GLU D 377 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 378 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 381 " --> pdb=" O ALA D 378 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASP D 382 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 385 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 387 " --> pdb=" O MET D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.659A pdb=" N ASP D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 400 through 404' Processing helix chain 'E' and resid 67 through 77 removed outlier: 3.637A pdb=" N HIS E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 101 Processing helix chain 'E' and resid 125 through 136 removed outlier: 3.551A pdb=" N ALA E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU E 130 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 135 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.581A pdb=" N LYS E 164 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 205 through 216 removed outlier: 4.454A pdb=" N LYS E 213 " --> pdb=" O GLN E 209 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 263 Processing helix chain 'E' and resid 283 through 289 removed outlier: 3.758A pdb=" N LEU E 287 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN E 289 " --> pdb=" O GLU E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 283 through 289' Processing helix chain 'E' and resid 292 through 298 removed outlier: 3.710A pdb=" N LYS E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 321 through 327 Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 352 through 365 Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.982A pdb=" N ARG E 373 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 378 " --> pdb=" O ILE E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'F' and resid 67 through 77 removed outlier: 3.792A pdb=" N TYR F 77 " --> pdb=" O HIS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 101 removed outlier: 3.630A pdb=" N LEU F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 100 " --> pdb=" O TYR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 136 removed outlier: 3.742A pdb=" N ALA F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.656A pdb=" N ILE F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 165 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 4.507A pdb=" N LYS F 213 " --> pdb=" O GLN F 209 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 226 No H-bonds generated for 'chain 'F' and resid 224 through 226' Processing helix chain 'F' and resid 254 through 261 removed outlier: 3.642A pdb=" N ARG F 261 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 Processing helix chain 'F' and resid 292 through 298 removed outlier: 3.583A pdb=" N ILE F 296 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS F 297 " --> pdb=" O GLU F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 319 through 327 removed outlier: 3.632A pdb=" N ILE F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 344 Processing helix chain 'F' and resid 352 through 365 removed outlier: 3.530A pdb=" N ALA F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 387 removed outlier: 3.682A pdb=" N VAL F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP F 382 " --> pdb=" O ALA F 378 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing sheet with id= A, first strand: chain 'A' and resid 311 through 313 removed outlier: 6.899A pdb=" N LEU A 116 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.744A pdb=" N ALA A 220 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 238 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.549A pdb=" N VAL A 397 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 410 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.955A pdb=" N ILE B 180 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 244 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE B 183 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 246 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 219 through 223 removed outlier: 4.066A pdb=" N ALA B 220 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 238 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 236 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.533A pdb=" N LYS B 395 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 312 through 314 Processing sheet with id= H, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.616A pdb=" N ILE C 398 " --> pdb=" O GLU C 349 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE C 412 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL C 396 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 410 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 180 through 184 removed outlier: 6.388A pdb=" N LEU D 244 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE D 183 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE D 246 " --> pdb=" O ILE D 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.518A pdb=" N ILE D 398 " --> pdb=" O GLU D 349 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 312 through 314 removed outlier: 3.503A pdb=" N ILE E 115 " --> pdb=" O PHE E 245 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 219 through 222 removed outlier: 4.036A pdb=" N ALA E 220 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 238 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 347 through 350 removed outlier: 3.522A pdb=" N GLU E 349 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.485A pdb=" N ILE F 180 " --> pdb=" O THR F 141 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU F 244 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ILE F 183 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE F 246 " --> pdb=" O ILE F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'F' and resid 347 through 350 removed outlier: 3.696A pdb=" N ILE F 398 " --> pdb=" O GLU F 349 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1164 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: 11.12 Time building geometry restraints manager: 27.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 16120 1.06 - 1.28: 2857 1.28 - 1.50: 6187 1.50 - 1.73: 7088 1.73 - 1.95: 59 Bond restraints: 32311 Sorted by residual: bond pdb=" C ILE D 301 " pdb=" N PRO D 302 " ideal model delta sigma weight residual 1.334 1.366 -0.032 1.51e-02 4.39e+03 4.47e+00 bond pdb=" N LEU A 64 " pdb=" CA LEU A 64 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N LEU F 64 " pdb=" CA LEU F 64 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.70e+00 bond pdb=" C PRO D 223 " pdb=" N PRO D 224 " ideal model delta sigma weight residual 1.335 1.350 -0.015 8.70e-03 1.32e+04 2.95e+00 bond pdb=" N UNK S 1 " pdb=" CA UNK S 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 ... (remaining 32306 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.65: 3063 107.65 - 114.78: 39670 114.78 - 121.90: 10479 121.90 - 129.02: 5472 129.02 - 136.15: 86 Bond angle restraints: 58770 Sorted by residual: angle pdb=" CA GLY F 206 " pdb=" C GLY F 206 " pdb=" N VAL F 207 " ideal model delta sigma weight residual 116.81 111.26 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" C ASN C 101 " pdb=" N GLY C 102 " pdb=" CA GLY C 102 " ideal model delta sigma weight residual 121.41 132.11 -10.70 1.96e+00 2.60e-01 2.98e+01 angle pdb=" N SER C 105 " pdb=" CA SER C 105 " pdb=" C SER C 105 " ideal model delta sigma weight residual 109.59 101.92 7.67 1.61e+00 3.86e-01 2.27e+01 angle pdb=" C GLY F 204 " pdb=" N GLU F 205 " pdb=" CA GLU F 205 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C GLU F 205 " pdb=" N GLY F 206 " pdb=" CA GLY F 206 " ideal model delta sigma weight residual 119.94 124.18 -4.24 1.11e+00 8.12e-01 1.46e+01 ... (remaining 58765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 13159 17.32 - 34.63: 1064 34.63 - 51.95: 213 51.95 - 69.26: 25 69.26 - 86.58: 11 Dihedral angle restraints: 14472 sinusoidal: 8013 harmonic: 6459 Sorted by residual: dihedral pdb=" CA LYS C 366 " pdb=" CB LYS C 366 " pdb=" CG LYS C 366 " pdb=" CD LYS C 366 " ideal model delta sinusoidal sigma weight residual -60.00 -119.14 59.14 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 194 " pdb=" CB ASP A 194 " pdb=" CG ASP A 194 " pdb=" OD1 ASP A 194 " ideal model delta sinusoidal sigma weight residual -30.00 -82.13 52.13 1 2.00e+01 2.50e-03 9.27e+00 dihedral pdb=" N ARG E 370 " pdb=" CA ARG E 370 " pdb=" CB ARG E 370 " pdb=" CG ARG E 370 " ideal model delta sinusoidal sigma weight residual -180.00 -129.30 -50.70 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 14469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1961 0.041 - 0.083: 441 0.083 - 0.124: 164 0.124 - 0.166: 31 0.166 - 0.207: 1 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CA ASP C 103 " pdb=" N ASP C 103 " pdb=" C ASP C 103 " pdb=" CB ASP C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE B 301 " pdb=" N ILE B 301 " pdb=" C ILE B 301 " pdb=" CB ILE B 301 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA SER C 105 " pdb=" N SER C 105 " pdb=" C SER C 105 " pdb=" CB SER C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2595 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 370 " 0.090 9.50e-02 1.11e+02 9.25e-02 1.73e+02 pdb=" NE ARG B 370 " 0.074 2.00e-02 2.50e+03 pdb=" CZ ARG B 370 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 370 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 370 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 370 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 370 " -0.058 2.00e-02 2.50e+03 pdb="HH21 ARG B 370 " -0.172 2.00e-02 2.50e+03 pdb="HH22 ARG B 370 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 195 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO E 196 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 328 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO F 329 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 329 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 329 " 0.028 5.00e-02 4.00e+02 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 161 2.01 - 2.65: 45151 2.65 - 3.30: 91772 3.30 - 3.95: 112184 3.95 - 4.60: 176602 Nonbonded interactions: 425870 Sorted by model distance: nonbonded pdb=" OD1 ASP C 399 " pdb=" HG SER C 401 " model vdw 1.357 1.850 nonbonded pdb=" HZ2 LYS C 112 " pdb=" O SER C 241 " model vdw 1.397 1.850 nonbonded pdb=" OD1 ASP E 144 " pdb=" HG1 THR E 146 " model vdw 1.425 1.850 nonbonded pdb=" O GLU F 263 " pdb=" HG1 THR F 264 " model vdw 1.429 1.850 nonbonded pdb=" O LEU C 326 " pdb=" HG1 THR C 334 " model vdw 1.434 1.850 ... (remaining 425865 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' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'B' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'C' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'D' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'E' and (resid 64 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 7 \ 5 through 149 or resid 157 through 194 or resid 202 through 225 or resid 233 thr \ ough 413)) selection = (chain 'F' and (resid 64 through 225 or resid 233 through 259 or (resid 260 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 261 through 413)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 0.470 Extract box with map and model: 3.430 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 101.000 Find NCS groups from input model: 1.660 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: 0.010 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: 110.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.004 0.040 16185 Z= 0.235 Angle : 0.713 10.700 21919 Z= 0.392 Chirality : 0.042 0.207 2598 Planarity : 0.004 0.076 2819 Dihedral : 12.431 81.962 6147 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -1.13 (0.17), residues: 2031 helix: -0.21 (0.16), residues: 770 sheet: -0.40 (0.30), residues: 272 loop : -1.23 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 95 PHE 0.014 0.001 PHE A 270 TYR 0.010 0.001 TYR E 93 ARG 0.013 0.001 ARG E 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.6383 time to fit residues: 376.7720 Evaluate side-chains 238 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 118 optimal weight: 0.1980 chunk 184 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 195 ASN A 225 GLN B 68 HIS B 167 GLN B 185 GLN B 208 GLN C 101 ASN D 260 HIS F 114 ASN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 ASN F 336 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16185 Z= 0.192 Angle : 0.532 5.766 21919 Z= 0.284 Chirality : 0.040 0.167 2598 Planarity : 0.004 0.046 2819 Dihedral : 7.473 60.919 2294 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2031 helix: 0.47 (0.17), residues: 803 sheet: -0.19 (0.31), residues: 280 loop : -1.04 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 68 PHE 0.018 0.001 PHE E 298 TYR 0.016 0.001 TYR E 93 ARG 0.007 0.001 ARG F 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 276 average time/residue: 0.6348 time to fit residues: 261.9185 Evaluate side-chains 208 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4101 time to fit residues: 3.9271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN C 95 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16185 Z= 0.228 Angle : 0.518 5.603 21919 Z= 0.269 Chirality : 0.039 0.144 2598 Planarity : 0.003 0.030 2819 Dihedral : 7.343 65.692 2294 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2031 helix: 0.34 (0.17), residues: 844 sheet: -0.15 (0.31), residues: 268 loop : -1.02 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 73 PHE 0.014 0.001 PHE E 298 TYR 0.014 0.001 TYR E 93 ARG 0.004 0.000 ARG F 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.5998 time to fit residues: 225.7801 Evaluate side-chains 194 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 GLN C 101 ASN C 331 ASN D 225 GLN D 260 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16185 Z= 0.317 Angle : 0.595 7.519 21919 Z= 0.307 Chirality : 0.040 0.155 2598 Planarity : 0.004 0.064 2819 Dihedral : 7.148 72.588 2294 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -1.06 (0.17), residues: 2031 helix: -0.26 (0.17), residues: 843 sheet: -0.20 (0.31), residues: 272 loop : -1.19 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS S 3 PHE 0.024 0.001 PHE E 298 TYR 0.026 0.002 TYR A 182 ARG 0.004 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.5800 time to fit residues: 202.7880 Evaluate side-chains 175 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS D 225 GLN E 338 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16185 Z= 0.279 Angle : 0.555 5.320 21919 Z= 0.287 Chirality : 0.040 0.144 2598 Planarity : 0.003 0.029 2819 Dihedral : 7.145 75.463 2294 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -1.23 (0.17), residues: 2031 helix: -0.44 (0.16), residues: 866 sheet: -0.32 (0.30), residues: 275 loop : -1.25 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 73 PHE 0.032 0.001 PHE B 245 TYR 0.013 0.001 TYR D 385 ARG 0.005 0.000 ARG E 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.5639 time to fit residues: 187.0866 Evaluate side-chains 169 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.075 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 115 optimal weight: 0.0670 chunk 48 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16185 Z= 0.182 Angle : 0.485 5.346 21919 Z= 0.249 Chirality : 0.039 0.144 2598 Planarity : 0.003 0.032 2819 Dihedral : 7.024 76.370 2294 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.06 % Allowed : 0.76 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 2031 helix: -0.08 (0.17), residues: 860 sheet: -0.24 (0.29), residues: 275 loop : -1.19 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 73 PHE 0.025 0.001 PHE B 245 TYR 0.011 0.001 TYR D 385 ARG 0.004 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 212 average time/residue: 0.5701 time to fit residues: 190.8210 Evaluate side-chains 174 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 2.730 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4185 time to fit residues: 3.9477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 122 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16185 Z= 0.190 Angle : 0.483 5.342 21919 Z= 0.247 Chirality : 0.039 0.145 2598 Planarity : 0.003 0.027 2819 Dihedral : 7.033 85.079 2294 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.18), residues: 2031 helix: -0.03 (0.17), residues: 868 sheet: -0.21 (0.30), residues: 270 loop : -1.12 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 73 PHE 0.027 0.001 PHE B 245 TYR 0.011 0.001 TYR A 182 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.5600 time to fit residues: 184.5392 Evaluate side-chains 170 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16185 Z= 0.242 Angle : 0.526 6.587 21919 Z= 0.271 Chirality : 0.039 0.141 2598 Planarity : 0.003 0.029 2819 Dihedral : 7.085 89.920 2294 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.47 % 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 (0.18), residues: 2031 helix: -0.23 (0.17), residues: 876 sheet: -0.22 (0.30), residues: 275 loop : -1.24 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 73 PHE 0.028 0.001 PHE B 245 TYR 0.012 0.001 TYR A 182 ARG 0.006 0.000 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 204 average time/residue: 0.5656 time to fit residues: 183.5760 Evaluate side-chains 169 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.818 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4707 time to fit residues: 4.3286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 172 optimal weight: 0.2980 chunk 181 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16185 Z= 0.161 Angle : 0.477 5.854 21919 Z= 0.243 Chirality : 0.039 0.142 2598 Planarity : 0.003 0.029 2819 Dihedral : 6.942 87.605 2294 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.18), residues: 2031 helix: 0.05 (0.17), residues: 873 sheet: -0.20 (0.31), residues: 257 loop : -1.07 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 73 PHE 0.021 0.001 PHE B 245 TYR 0.011 0.001 TYR A 182 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4062 Ramachandran restraints generated. 2031 Oldfield, 0 Emsley, 2031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 74 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.5636 time to fit residues: 184.4745 Evaluate side-chains 171 residues out of total 1709 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 68.6038 > 50: distance: 111 - 290: 30.638 distance: 114 - 287: 21.382 distance: 159 - 192: 24.536 distance: 167 - 176: 24.587 distance: 168 - 211: 29.849 distance: 176 - 177: 27.678 distance: 176 - 183: 23.090 distance: 177 - 178: 20.118 distance: 177 - 180: 17.546 distance: 177 - 184: 30.062 distance: 178 - 179: 21.477 distance: 178 - 192: 21.001 distance: 180 - 181: 12.065 distance: 180 - 182: 16.585 distance: 180 - 185: 19.051 distance: 181 - 186: 18.227 distance: 181 - 187: 24.918 distance: 181 - 188: 10.049 distance: 182 - 190: 6.691 distance: 182 - 191: 20.468 distance: 192 - 193: 8.916 distance: 192 - 200: 41.375 distance: 193 - 194: 28.629 distance: 193 - 196: 19.452 distance: 193 - 201: 8.535 distance: 194 - 195: 7.891 distance: 194 - 211: 56.744 distance: 196 - 197: 38.119 distance: 196 - 198: 25.878 distance: 196 - 202: 21.022 distance: 197 - 199: 13.197 distance: 197 - 203: 10.669 distance: 197 - 204: 12.197 distance: 198 - 205: 10.331 distance: 198 - 206: 10.173 distance: 198 - 207: 9.173 distance: 199 - 208: 11.936 distance: 199 - 209: 10.989 distance: 199 - 210: 15.273 distance: 211 - 212: 19.751 distance: 211 - 219: 27.962 distance: 212 - 213: 20.211 distance: 212 - 215: 18.795 distance: 212 - 220: 29.873 distance: 213 - 214: 20.684 distance: 213 - 223: 20.553 distance: 215 - 216: 30.815 distance: 215 - 221: 8.708 distance: 215 - 222: 29.195 distance: 216 - 217: 26.141 distance: 216 - 218: 20.444 distance: 223 - 224: 20.084 distance: 223 - 227: 32.269 distance: 224 - 225: 32.129 distance: 224 - 228: 48.789 distance: 224 - 229: 18.657 distance: 225 - 226: 22.774 distance: 225 - 230: 7.531 distance: 230 - 231: 44.224 distance: 230 - 239: 12.133 distance: 231 - 232: 24.823 distance: 231 - 234: 14.954 distance: 231 - 240: 14.909 distance: 232 - 233: 18.736 distance: 232 - 247: 56.378 distance: 234 - 235: 11.072 distance: 234 - 241: 14.106 distance: 234 - 242: 28.136 distance: 235 - 236: 13.400 distance: 235 - 243: 15.865 distance: 235 - 244: 10.484 distance: 236 - 237: 21.108 distance: 236 - 238: 8.724 distance: 238 - 245: 17.295 distance: 238 - 246: 16.845 distance: 247 - 248: 41.041 distance: 247 - 253: 4.674 distance: 248 - 249: 41.261 distance: 248 - 251: 20.611 distance: 248 - 254: 27.222 distance: 249 - 250: 21.849 distance: 249 - 258: 40.728 distance: 251 - 252: 16.218 distance: 251 - 255: 17.246 distance: 251 - 256: 14.212 distance: 252 - 257: 7.278 distance: 258 - 259: 45.739 distance: 258 - 267: 44.955 distance: 259 - 260: 33.448 distance: 259 - 262: 44.266 distance: 259 - 268: 36.428 distance: 260 - 261: 41.943 distance: 260 - 273: 20.792 distance: 262 - 263: 27.077 distance: 262 - 269: 46.974 distance: 262 - 270: 27.382 distance: 263 - 264: 49.032 distance: 263 - 271: 36.288 distance: 263 - 272: 42.263 distance: 264 - 265: 25.855 distance: 264 - 266: 15.125 distance: 273 - 274: 25.075 distance: 273 - 279: 32.314 distance: 274 - 275: 20.130 distance: 274 - 277: 13.524 distance: 274 - 280: 13.127 distance: 275 - 276: 13.727 distance: 275 - 287: 42.967 distance: 277 - 278: 10.897 distance: 277 - 281: 20.309 distance: 277 - 282: 26.798 distance: 278 - 279: 30.878 distance: 278 - 283: 22.672 distance: 278 - 284: 15.611 distance: 279 - 285: 34.949 distance: 279 - 286: 38.267 distance: 287 - 288: 16.660 distance: 287 - 295: 10.004 distance: 288 - 289: 43.244 distance: 288 - 291: 20.122 distance: 288 - 296: 27.078 distance: 289 - 290: 9.018 distance: 289 - 306: 45.183 distance: 291 - 292: 8.375 distance: 291 - 297: 24.118 distance: 291 - 298: 22.331 distance: 292 - 293: 19.172 distance: 292 - 294: 10.348 distance: 292 - 299: 13.926 distance: 293 - 300: 8.508 distance: 293 - 301: 5.853 distance: 293 - 302: 5.093 distance: 294 - 303: 15.585 distance: 294 - 304: 5.294 distance: 294 - 305: 7.832 distance: 306 - 307: 14.698 distance: 306 - 314: 24.359 distance: 307 - 308: 7.012 distance: 307 - 310: 7.714 distance: 307 - 315: 8.823 distance: 308 - 309: 17.733 distance: 308 - 325: 8.792 distance: 310 - 311: 12.295 distance: 310 - 316: 22.135 distance: 310 - 317: 11.943 distance: 311 - 312: 12.229 distance: 311 - 313: 24.801 distance: 311 - 318: 12.639 distance: 312 - 319: 8.299 distance: 312 - 320: 6.708 distance: 312 - 321: 5.396 distance: 313 - 322: 11.641 distance: 313 - 323: 6.642 distance: 313 - 324: 11.352