Starting phenix.real_space_refine on Mon Aug 5 17:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/08_2024/6ugf_20763_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/08_2024/6ugf_20763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/08_2024/6ugf_20763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/08_2024/6ugf_20763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/08_2024/6ugf_20763_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugf_20763/08_2024/6ugf_20763_neut.cif" } resolution = 4.2 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= 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 15 5.49 5 Mg 4 5.21 5 S 63 5.16 5 C 8776 2.51 5 N 2430 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 244": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A ASP 387": "OD1" <-> "OD2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D ASP 295": "OD1" <-> "OD2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 295": "OD1" <-> "OD2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 194": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 431": "OE1" <-> "OE2" Residue "G GLU 4": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13874 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2231 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2273 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2297 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2318 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2306 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2186 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.63, per 1000 atoms: 0.55 Number of scatterers: 13874 At special positions: 0 Unit cell: (127.44, 139.32, 117.72, 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 63 16.00 P 15 15.00 Mg 4 11.99 O 2586 8.00 N 2430 7.00 C 8776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.5 seconds 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3486 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 6 sheets defined 49.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 198 through 209 removed outlier: 3.654A pdb=" N LYS A 202 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.807A pdb=" N ARG A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.887A pdb=" N ARG A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.548A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 351' Processing helix chain 'A' and resid 363 through 375 removed outlier: 4.319A pdb=" N ARG A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 392 removed outlier: 3.533A pdb=" N LEU A 389 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 416 removed outlier: 4.137A pdb=" N VAL A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.582A pdb=" N ALA A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.908A pdb=" N PHE A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.521A pdb=" N GLY B 162 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 163 " --> pdb=" O SER B 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 163' Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.688A pdb=" N VAL B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.751A pdb=" N LYS B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.534A pdb=" N ILE B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.650A pdb=" N PHE B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.816A pdb=" N LYS B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.840A pdb=" N THR B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 415 removed outlier: 3.647A pdb=" N ARG B 415 " --> pdb=" O ASN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.947A pdb=" N GLU B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 470 removed outlier: 3.593A pdb=" N LYS B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.834A pdb=" N GLY C 162 " --> pdb=" O ASN C 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 163 " --> pdb=" O SER C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 171 through 182 removed outlier: 3.584A pdb=" N VAL C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 207 Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.706A pdb=" N LEU C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 240 through 249 removed outlier: 3.506A pdb=" N ARG C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 285 removed outlier: 3.620A pdb=" N ARG C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 4.442A pdb=" N LYS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.710A pdb=" N LYS C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 394 removed outlier: 3.748A pdb=" N LEU C 389 " --> pdb=" O ASN C 385 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 411 removed outlier: 3.587A pdb=" N SER C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 434 Processing helix chain 'C' and resid 439 through 448 removed outlier: 3.894A pdb=" N PHE C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.541A pdb=" N GLY D 162 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 163' Processing helix chain 'D' and resid 171 through 180 removed outlier: 3.870A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 removed outlier: 3.900A pdb=" N ASP D 194 " --> pdb=" O SER D 191 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 195 " --> pdb=" O LEU D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 195' Processing helix chain 'D' and resid 198 through 207 Processing helix chain 'D' and resid 210 through 215 removed outlier: 4.071A pdb=" N LEU D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 removed outlier: 3.731A pdb=" N ILE D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 285 removed outlier: 3.880A pdb=" N ARG D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 4.152A pdb=" N LEU D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 366 through 375 Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 397 through 414 removed outlier: 3.648A pdb=" N VAL D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 434 removed outlier: 3.783A pdb=" N LEU D 433 " --> pdb=" O ALA D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 450 removed outlier: 3.909A pdb=" N PHE D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 470 removed outlier: 3.577A pdb=" N LYS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.564A pdb=" N GLY E 162 " --> pdb=" O ASN E 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP E 163 " --> pdb=" O SER E 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 163' Processing helix chain 'E' and resid 171 through 180 removed outlier: 3.877A pdb=" N VAL E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 207 Processing helix chain 'E' and resid 209 through 215 removed outlier: 3.695A pdb=" N LEU E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.973A pdb=" N ARG E 223 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER E 224 " --> pdb=" O GLY E 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 220 through 224' Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 269 through 285 removed outlier: 4.135A pdb=" N ALA E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 Processing helix chain 'E' and resid 309 through 322 removed outlier: 4.547A pdb=" N ASP E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 345 removed outlier: 3.915A pdb=" N LEU E 345 " --> pdb=" O PRO E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 351 Processing helix chain 'E' and resid 363 through 375 Processing helix chain 'E' and resid 385 through 393 removed outlier: 3.814A pdb=" N LEU E 389 " --> pdb=" O ASN E 385 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 416 removed outlier: 3.705A pdb=" N SER E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR E 416 " --> pdb=" O VAL E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 434 removed outlier: 3.861A pdb=" N LYS E 434 " --> pdb=" O MET E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 449 removed outlier: 3.813A pdb=" N PHE E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 470 Processing helix chain 'F' and resid 159 through 163 removed outlier: 3.743A pdb=" N GLY F 162 " --> pdb=" O ASN F 159 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP F 163 " --> pdb=" O SER F 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 163' Processing helix chain 'F' and resid 173 through 180 Processing helix chain 'F' and resid 191 through 195 Processing helix chain 'F' and resid 198 through 207 removed outlier: 3.789A pdb=" N LYS F 202 " --> pdb=" O MET F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 215 removed outlier: 3.952A pdb=" N LEU F 214 " --> pdb=" O THR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 250 removed outlier: 4.050A pdb=" N SER F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 284 removed outlier: 3.761A pdb=" N VAL F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 removed outlier: 4.147A pdb=" N LEU F 297 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 321 removed outlier: 3.748A pdb=" N LYS F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 353 removed outlier: 4.094A pdb=" N ARG F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 353 " --> pdb=" O LEU F 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 353' Processing helix chain 'F' and resid 364 through 375 Processing helix chain 'F' and resid 385 through 392 Processing helix chain 'F' and resid 399 through 416 removed outlier: 4.344A pdb=" N LEU F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR F 416 " --> pdb=" O VAL F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 432 Processing helix chain 'F' and resid 439 through 448 removed outlier: 4.046A pdb=" N PHE F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 470 removed outlier: 4.290A pdb=" N MET F 459 " --> pdb=" O GLY F 455 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER F 468 " --> pdb=" O GLU F 464 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 231 removed outlier: 3.615A pdb=" N ALA A 338 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 256 through 257 removed outlier: 4.025A pdb=" N ASP B 292 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 289 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ALA B 338 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE B 291 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 228 through 232 removed outlier: 3.548A pdb=" N THR C 339 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 338 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.879A pdb=" N SER D 287 " --> pdb=" O PHE D 334 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU D 336 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE D 289 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ALA D 338 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE D 291 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE D 255 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP D 292 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL D 257 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 254 through 257 removed outlier: 6.499A pdb=" N PHE E 255 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASP E 292 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL E 257 " --> pdb=" O ASP E 292 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE E 289 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ALA E 338 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE E 291 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 254 through 257 removed outlier: 6.789A pdb=" N PHE F 255 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP F 292 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL F 257 " --> pdb=" O ASP F 292 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER F 287 " --> pdb=" O PHE F 334 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU F 336 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE F 289 " --> pdb=" O LEU F 336 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ALA F 338 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE F 291 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU F 231 " --> pdb=" O THR F 339 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL F 230 " --> pdb=" O ILE F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 495 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 5.18 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: 4485 1.34 - 1.45: 2238 1.45 - 1.57: 7269 1.57 - 1.69: 25 1.69 - 1.81: 109 Bond restraints: 14126 Sorted by residual: bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.63e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.36e+01 ... (remaining 14121 not shown) Histogram of bond angle deviations from ideal: 98.52 - 106.38: 431 106.38 - 114.24: 8318 114.24 - 122.10: 7887 122.10 - 129.95: 2471 129.95 - 137.81: 86 Bond angle restraints: 19193 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 115.98 23.89 1.00e+00 1.00e+00 5.71e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 113.58 23.25 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 116.67 23.20 1.00e+00 1.00e+00 5.38e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 118.32 21.55 1.00e+00 1.00e+00 4.64e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 115.32 21.51 1.00e+00 1.00e+00 4.62e+02 ... (remaining 19188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 7669 17.47 - 34.95: 747 34.95 - 52.42: 123 52.42 - 69.90: 24 69.90 - 87.37: 16 Dihedral angle restraints: 8579 sinusoidal: 3219 harmonic: 5360 Sorted by residual: dihedral pdb=" CA PRO A 362 " pdb=" C PRO A 362 " pdb=" N ASP A 363 " pdb=" CA ASP A 363 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER C 453 " pdb=" C SER C 453 " pdb=" N ALA C 454 " pdb=" CA ALA C 454 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLY A 305 " pdb=" C GLY A 305 " pdb=" N GLU A 306 " pdb=" CA GLU A 306 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 8576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1559 0.052 - 0.103: 546 0.103 - 0.155: 105 0.155 - 0.206: 15 0.206 - 0.258: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C1' ATP B 501 " pdb=" C2' ATP B 501 " pdb=" N9 ATP B 501 " pdb=" O4' ATP B 501 " both_signs ideal model delta sigma weight residual False 2.41 2.67 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE B 341 " pdb=" CA ILE B 341 " pdb=" CG1 ILE B 341 " pdb=" CG2 ILE B 341 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE A 196 " pdb=" CA ILE A 196 " pdb=" CG1 ILE A 196 " pdb=" CG2 ILE A 196 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2227 not shown) Planarity restraints: 2443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 211 " -0.048 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO F 212 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 212 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 212 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 285 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.83e+00 pdb=" N PRO A 286 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO C 212 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.036 5.00e-02 4.00e+02 ... (remaining 2440 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 162 2.62 - 3.19: 11523 3.19 - 3.76: 20242 3.76 - 4.33: 25858 4.33 - 4.90: 42466 Nonbonded interactions: 100251 Sorted by model distance: nonbonded pdb=" O1G ATP E 501 " pdb="MG MG E 502 " model vdw 2.046 2.170 nonbonded pdb=" O3B ATP C 501 " pdb="MG MG C 502 " model vdw 2.050 2.170 nonbonded pdb=" O2G ATP B 501 " pdb="MG MG B 502 " model vdw 2.063 2.170 nonbonded pdb=" O2B ATP B 501 " pdb="MG MG B 502 " model vdw 2.069 2.170 nonbonded pdb=" O3G ATP D 501 " pdb="MG MG D 502 " model vdw 2.075 2.170 ... (remaining 100246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 189 or (resid 190 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 259 or (resid 260 and (name N or name CA or name C or name O or name CB \ )) or resid 261 through 294 or (resid 295 and (name N or name CA or name C or n \ ame O or name CB )) or resid 296 through 303 or (resid 304 and (name N or name C \ A or name C or name O or name CB )) or resid 305 through 322 or resid 332 throug \ h 343 or (resid 344 and (name N or name CA or name C or name O or name CB )) or \ resid 345 through 360 or (resid 361 and (name N or name CA or name C or name O o \ r name CB )) or resid 362 or (resid 363 and (name N or name CA or name C or name \ O or name CB )) or resid 364 through 366 or (resid 367 and (name N or name CA o \ r name C or name O or name CB )) or resid 368 or (resid 369 and (name N or name \ CA or name C or name O or name CB )) or resid 370 through 371 or (resid 372 thro \ ugh 373 and (name N or name CA or name C or name O or name CB )) or resid 374 or \ (resid 375 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 6 through 377 or (resid 378 and (name N or name CA or name C or name O or name C \ B )) or resid 379 or (resid 380 and (name N or name CA or name C or name O or na \ me CB )) or resid 381 or (resid 382 through 385 and (name N or name CA or name C \ or name O or name CB )) or resid 386 or (resid 387 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 399 or (resid 400 \ and (name N or name CA or name C or name O or name CB )) or resid 401 through 40 \ 5 or (resid 406 and (name N or name CA or name C or name O or name CB )) or resi \ d 407 through 413 or (resid 414 and (name N or name CA or name C or name O or na \ me CB )) or resid 415 through 417 or (resid 418 through 419 and (name N or name \ CA or name C or name O or name CB )) or resid 420 or (resid 421 through 422 and \ (name N or name CA or name C or name O or name CB )) or resid 423 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 8 or (resid 439 and (name N or name CA or name C or name O or name CB )) or resi \ d 440 through 443 or (resid 444 through 446 and (name N or name CA or name C or \ name O or name CB )) or resid 447 or (resid 448 through 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 457 or (resid 458 thro \ ugh 464 and (name N or name CA or name C or name O or name CB )) or resid 465 th \ rough 466 or (resid 467 through 468 and (name N or name CA or name C or name O o \ r name CB )) or resid 469 through 472)) selection = (chain 'B' and (resid 156 through 167 or (resid 168 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 182 or (resid 188 through 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 or (resid 193 through 194 and (name N or name CA o \ r name C or name O or name CB )) or resid 195 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 216 or (re \ sid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 th \ rough 222 or (resid 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 226 or (resid 227 through 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 243 or (resid 244 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 245 through \ 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or r \ esid 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 268 or (resid 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or n \ ame O or name CB )) or resid 272 through 278 or (resid 279 and (name N or name C \ A or name C or name O or name CB )) or resid 280 through 294 or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or resid 296 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ or (resid 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 or (resid 308 through 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 314 or (resid 315 through 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 318 or (resid 319 and ( \ name N or name CA or name C or name O or name CB )) or resid 320 through 322 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 or (resid 346 through 348 and (name N or name CA or name C or n \ ame O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 through 360 or (res \ id 361 and (name N or name CA or name C or name O or name CB )) or resid 362 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 through 387 or \ (resid 388 through 394 and (name N or name CA or name C or name O or name CB )) \ or resid 395 through 399 or (resid 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 405 or (resid 406 and (name N or name CA or \ name C or name O or name CB )) or resid 407 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 417 or (res \ id 418 through 419 and (name N or name CA or name C or name O or name CB )) or r \ esid 420 or (resid 421 through 422 and (name N or name CA or name C or name O or \ name CB )) or resid 423 through 430 or (resid 431 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 435 or (resid 436 t \ hrough 437 and (name N or name CA or name C or name O or name CB )) or resid 438 \ through 443 or (resid 444 through 446 and (name N or name CA or name C or name \ O or name CB )) or resid 447 or (resid 448 through 450 and (name N or name CA or \ name C or name O or name CB )) or resid 451 through 452 or (resid 453 through 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 457 or (resid 458 through 464 and (name N or name CA or name C or name O or nam \ e CB )) or resid 465 through 466 or (resid 467 through 468 and (name N or name C \ A or name C or name O or name CB )) or resid 469 through 471 or (resid 472 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 through 193 or (resid 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 222 or (resid 223 and (name N or name CA or name C or name O or na \ me CB )) or resid 224 through 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 258 or (resid 259 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 268 or (resid 269 and (name N or name CA or \ name C or name O or name CB )) or resid 270 or (resid 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 278 or (resid 279 and ( \ name N or name CA or name C or name O or name CB )) or resid 280 through 294 or \ (resid 295 and (name N or name CA or name C or name O or name CB )) or resid 296 \ through 303 or (resid 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 or (resid 306 and (name N or name CA or name C or name O or nam \ e CB )) or resid 307 or (resid 308 through 309 and (name N or name CA or name C \ or name O or name CB )) or resid 310 through 314 or (resid 315 through 316 and ( \ name N or name CA or name C or name O or name CB )) or resid 317 through 318 or \ (resid 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 322 or (resid 332 and (name N or name CA or name C or name O or name CB \ )) or resid 333 through 343 or (resid 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 or (resid 346 through 348 and (name N or name C \ A or name C or name O or name CB )) or resid 349 through 354 or (resid 355 throu \ gh 356 and (name N or name CA or name C or name O or name CB )) or resid 357 thr \ ough 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 366 or (resid 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name C or n \ ame O or name CB )) or resid 370 through 371 or (resid 372 through 373 and (name \ N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 and ( \ name N or name CA or name C or name O or name CB )) or resid 376 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 through 382 or (resid 383 through 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 387 or (resid 388 through 394 and (name \ N or name CA or name C or name O or name CB )) or resid 395 through 405 or (res \ id 406 and (name N or name CA or name C or name O or name CB )) or resid 407 thr \ ough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 420 or (resid 421 through 422 and (name N or name CA or nam \ e C or name O or name CB )) or resid 423 through 430 or (resid 431 through 432 a \ nd (name N or name CA or name C or name O or name CB )) or resid 433 through 435 \ or (resid 436 through 437 and (name N or name CA or name C or name O or name CB \ )) or resid 438 or (resid 439 and (name N or name CA or name C or name O or nam \ e CB )) or resid 440 through 443 or (resid 444 through 446 and (name N or name C \ A or name C or name O or name CB )) or resid 447 or (resid 448 through 450 and ( \ name N or name CA or name C or name O or name CB )) or resid 451 through 452 or \ (resid 453 through 454 and (name N or name CA or name C or name O or name CB )) \ or resid 455 through 456 or (resid 457 through 464 and (name N or name CA or nam \ e C or name O or name CB )) or resid 465 through 467 or (resid 468 and (name N o \ r name CA or name C or name O or name CB )) or resid 469 through 472)) selection = (chain 'D' and (resid 156 through 175 or (resid 176 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 189 or (resid 190 \ through 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 or (resid 193 through 194 and (name N or name CA or name C or name O or name C \ B )) or resid 195 through 199 or (resid 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB )) or resid 221 through 222 or (resid 223 and \ (name N or name CA or name C or name O or name CB )) or resid 224 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B or name CG )) or resid 245 through 248 or (resid 249 and (name N or name CA or \ name C or name O or name CB )) or resid 250 or (resid 251 and (name N or name C \ A or name C or name O or name CB )) or resid 252 through 258 or (resid 259 throu \ gh 260 and (name N or name CA or name C or name O or name CB )) or resid 261 thr \ ough 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) \ or resid 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 294 or (resid 295 and (name N or name C \ A or name C or name O or name CB )) or resid 296 through 303 or (resid 304 and ( \ name N or name CA or name C or name O or name CB )) or resid 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 or (resid 3 \ 08 through 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 314 or (resid 315 through 316 and (name N or name CA or name C or n \ ame O or name CB )) or resid 317 through 318 or (resid 319 and (name N or name C \ A or name C or name O or name CB )) or resid 320 through 322 or (resid 332 and ( \ name N or name CA or name C or name O or name CB )) or resid 333 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 345 \ through 346 or (resid 347 through 348 and (name N or name CA or name C or name \ O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 360 or (resid 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 or (res \ id 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 or (resid 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 381 or (resid 3 \ 82 through 385 and (name N or name CA or name C or name O or name CB )) or resid \ 386 or (resid 387 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 through 422 and (name N or name CA or name C or n \ ame O or name CB )) or resid 423 through 430 or (resid 431 through 432 and (name \ N or name CA or name C or name O or name CB )) or resid 433 through 436 or (res \ id 437 and (name N or name CA or name C or name O or name CB )) or resid 438 or \ (resid 439 and (name N or name CA or name C or name O or name CB )) or resid 440 \ through 447 or (resid 448 through 450 and (name N or name CA or name C or name \ O or name CB )) or resid 451 through 457 or (resid 458 through 464 and (name N o \ r name CA or name C or name O or name CB )) or resid 465 through 467 or (resid 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 through \ 472)) selection = (chain 'E' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 226 or (resid 227 \ through 228 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 9 or (resid 230 and (name N or name CA or name C or name O or name CB )) or resi \ d 231 through 243 or (resid 244 and (name N or name CA or name C or name O or na \ me CB or name CG )) or resid 245 through 248 or (resid 249 and (name N or name C \ A or name C or name O or name CB )) or resid 250 or (resid 251 and (name N or na \ me CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 t \ hrough 260 and (name N or name CA or name C or name O or name CB )) or resid 261 \ through 268 or (resid 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 or (resid 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 294 or (resid 295 and (name N or na \ me CA or name C or name O or name CB )) or resid 296 through 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 through 314 \ or (resid 315 through 316 and (name N or name CA or name C or name O or name CB \ )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 322 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 346 or \ (resid 347 through 348 and (name N or name CA or name C or name O or name CB )) \ or resid 349 through 354 or (resid 355 through 356 and (name N or name CA or nam \ e C or name O or name CB )) or resid 357 through 360 or (resid 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 through 366 or (resid 3 \ 67 and (name N or name CA or name C or name O or name CB )) or resid 368 or (res \ id 369 and (name N or name CA or name C or name O or name CB )) or resid 370 thr \ ough 371 or (resid 372 through 373 and (name N or name CA or name C or name O or \ name CB )) or resid 374 or (resid 375 and (name N or name CA or name C or name \ O or name CB )) or resid 376 through 377 or (resid 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 383 or (resid 384 through 3 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 388 or (resid 389 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 430 or (resid 431 through 432 and (name N or name CA or \ name C or name O or name CB )) or resid 433 through 436 or (resid 437 and (name \ N or name CA or name C or name O or name CB )) or resid 438 or (resid 439 and ( \ name N or name CA or name C or name O or name CB )) or resid 440 through 449 or \ (resid 450 and (name N or name CA or name C or name O or name CB )) or resid 451 \ through 452 or (resid 453 through 454 and (name N or name CA or name C or name \ O or name CB )) or resid 455 through 457 or (resid 458 through 464 and (name N o \ r name CA or name C or name O or name CB )) or resid 465 through 467 or (resid 4 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 469 through \ 472)) selection = (chain 'F' and (resid 156 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 192 or (resid 193 through 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 through 219 or (resid 220 and (name N or name CA o \ r name C or name O or name CB )) or resid 221 through 222 or (resid 223 and (nam \ e N or name CA or name C or name O or name CB )) or resid 224 through 226 or (re \ sid 227 through 228 and (name N or name CA or name C or name O or name CB )) or \ resid 229 or (resid 230 and (name N or name CA or name C or name O or name CB )) \ or resid 231 through 258 or (resid 259 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 270 or (resid 271 and (name N \ or name CA or name C or name O or name CB )) or resid 272 through 303 or (resid \ 304 and (name N or name CA or name C or name O or name CB )) or resid 305 throug \ h 314 or (resid 315 through 316 and (name N or name CA or name C or name O or na \ me CB )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 322 or resid 332 through 345 or (r \ esid 346 through 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 through 354 or (resid 355 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 through 399 or (resid 400 and (name N or \ name CA or name C or name O or name CB )) or resid 401 through 417 or (resid 418 \ through 419 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 20 or (resid 421 through 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 430 or (resid 431 through 432 and (name N or name CA \ or name C or name O or name CB )) or resid 433 through 443 or (resid 444 through \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 or (r \ esid 448 through 450 and (name N or name CA or name C or name O or name CB )) or \ resid 451 through 452 or (resid 453 through 454 and (name N or name CA or name \ C or name O or name CB )) or resid 455 through 472)) } 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: 2.250 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.370 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.060 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 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 0.076 14126 Z= 0.517 Angle : 1.109 23.889 19193 Z= 0.767 Chirality : 0.054 0.258 2230 Planarity : 0.007 0.071 2443 Dihedral : 14.483 87.371 5093 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.97 % Favored : 93.92 % Rotamer: Outliers : 0.30 % Allowed : 9.10 % Favored : 90.59 % 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: -4.55 (0.14), residues: 1826 helix: -3.10 (0.12), residues: 785 sheet: -2.15 (0.36), residues: 180 loop : -3.09 (0.16), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 226 HIS 0.006 0.001 HIS A 307 PHE 0.022 0.002 PHE C 353 TYR 0.019 0.002 TYR B 173 ARG 0.010 0.001 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 1.656 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: B 300 GLN cc_start: 0.8026 (tp40) cc_final: 0.7687 (mm110) REVERT: B 411 ASN cc_start: 0.9410 (t0) cc_final: 0.9149 (t0) REVERT: D 295 ASP cc_start: 0.8404 (p0) cc_final: 0.8128 (p0) REVERT: F 419 LYS cc_start: 0.6755 (mttp) cc_final: 0.6132 (mptt) outliers start: 4 outliers final: 0 residues processed: 182 average time/residue: 0.2589 time to fit residues: 68.7931 Evaluate side-chains 110 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 320 GLN A 340 ASN B 206 HIS B 307 HIS B 440 ASN D 203 GLN D 340 ASN F 199 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14126 Z= 0.164 Angle : 0.555 9.643 19193 Z= 0.291 Chirality : 0.040 0.206 2230 Planarity : 0.005 0.056 2443 Dihedral : 9.731 82.984 2156 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.15 % Allowed : 3.09 % Favored : 96.76 % 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: -2.92 (0.17), residues: 1826 helix: -1.34 (0.17), residues: 813 sheet: -1.42 (0.37), residues: 184 loop : -2.66 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 343 HIS 0.006 0.001 HIS B 206 PHE 0.019 0.001 PHE F 317 TYR 0.008 0.001 TYR A 284 ARG 0.006 0.000 ARG F 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 300 GLN cc_start: 0.8090 (tp40) cc_final: 0.7742 (mm110) REVERT: B 411 ASN cc_start: 0.9445 (t0) cc_final: 0.9119 (t0) REVERT: B 459 MET cc_start: 0.7428 (ptm) cc_final: 0.7168 (ppp) REVERT: C 357 ILE cc_start: 0.9499 (mt) cc_final: 0.9002 (tp) REVERT: D 295 ASP cc_start: 0.8452 (p0) cc_final: 0.8135 (p0) REVERT: F 365 ASP cc_start: 0.8395 (p0) cc_final: 0.7950 (p0) REVERT: F 419 LYS cc_start: 0.6712 (mttp) cc_final: 0.6218 (mptt) outliers start: 2 outliers final: 0 residues processed: 168 average time/residue: 0.2297 time to fit residues: 58.2631 Evaluate side-chains 116 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN D 158 GLN E 320 GLN F 206 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14126 Z= 0.145 Angle : 0.510 9.816 19193 Z= 0.262 Chirality : 0.039 0.169 2230 Planarity : 0.004 0.048 2443 Dihedral : 9.242 83.575 2156 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.18), residues: 1826 helix: -0.64 (0.18), residues: 813 sheet: -1.00 (0.38), residues: 186 loop : -2.32 (0.19), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 343 HIS 0.004 0.001 HIS C 307 PHE 0.013 0.001 PHE B 219 TYR 0.006 0.001 TYR B 386 ARG 0.005 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 300 GLN cc_start: 0.8006 (tp40) cc_final: 0.7542 (mm110) REVERT: B 411 ASN cc_start: 0.9468 (t0) cc_final: 0.9153 (t0) REVERT: B 459 MET cc_start: 0.7605 (ptm) cc_final: 0.7139 (ppp) REVERT: D 295 ASP cc_start: 0.8499 (p0) cc_final: 0.8175 (p0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2056 time to fit residues: 47.4150 Evaluate side-chains 110 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.0980 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 0.0980 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN B 158 GLN B 440 ASN E 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14126 Z= 0.127 Angle : 0.489 9.344 19193 Z= 0.248 Chirality : 0.038 0.150 2230 Planarity : 0.004 0.046 2443 Dihedral : 8.770 87.654 2156 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.14 % 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: -1.47 (0.19), residues: 1826 helix: -0.04 (0.19), residues: 802 sheet: -0.63 (0.39), residues: 188 loop : -2.00 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 226 HIS 0.003 0.001 HIS C 307 PHE 0.009 0.001 PHE B 278 TYR 0.007 0.001 TYR B 173 ARG 0.003 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7928 (ptm160) cc_final: 0.7512 (mmm160) REVERT: A 375 MET cc_start: 0.7892 (ttm) cc_final: 0.7681 (ttm) REVERT: B 411 ASN cc_start: 0.9496 (t0) cc_final: 0.9201 (t0) REVERT: B 459 MET cc_start: 0.7461 (ptm) cc_final: 0.7181 (ppp) REVERT: D 295 ASP cc_start: 0.8452 (p0) cc_final: 0.8077 (p0) REVERT: D 375 MET cc_start: 0.8679 (tpp) cc_final: 0.7944 (tpp) REVERT: D 400 ASP cc_start: 0.7784 (m-30) cc_final: 0.7578 (m-30) outliers start: 1 outliers final: 1 residues processed: 156 average time/residue: 0.2331 time to fit residues: 55.3878 Evaluate side-chains 108 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 0.0970 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14126 Z= 0.197 Angle : 0.524 9.089 19193 Z= 0.266 Chirality : 0.040 0.257 2230 Planarity : 0.004 0.044 2443 Dihedral : 8.751 87.199 2156 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: -1.07 (0.20), residues: 1826 helix: 0.31 (0.19), residues: 809 sheet: -0.45 (0.39), residues: 189 loop : -1.81 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 343 HIS 0.005 0.001 HIS C 307 PHE 0.009 0.001 PHE C 353 TYR 0.013 0.001 TYR D 170 ARG 0.004 0.000 ARG E 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.7969 (ptm160) cc_final: 0.7634 (mmm160) REVERT: B 411 ASN cc_start: 0.9494 (t0) cc_final: 0.9192 (t0) REVERT: B 459 MET cc_start: 0.7595 (ptm) cc_final: 0.7175 (ppp) REVERT: D 295 ASP cc_start: 0.8383 (p0) cc_final: 0.8072 (p0) REVERT: D 400 ASP cc_start: 0.7844 (m-30) cc_final: 0.7593 (m-30) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2133 time to fit residues: 43.9776 Evaluate side-chains 104 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 93 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN B 158 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14126 Z= 0.274 Angle : 0.564 9.444 19193 Z= 0.289 Chirality : 0.041 0.204 2230 Planarity : 0.004 0.043 2443 Dihedral : 9.149 89.645 2156 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -0.91 (0.20), residues: 1826 helix: 0.40 (0.19), residues: 809 sheet: -0.51 (0.38), residues: 194 loop : -1.65 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 266 HIS 0.005 0.001 HIS C 307 PHE 0.012 0.001 PHE C 317 TYR 0.017 0.001 TYR D 284 ARG 0.003 0.000 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7802 (mmm160) REVERT: B 411 ASN cc_start: 0.9484 (t0) cc_final: 0.9184 (t0) REVERT: B 459 MET cc_start: 0.7763 (ptm) cc_final: 0.7308 (ppp) REVERT: D 295 ASP cc_start: 0.8371 (p0) cc_final: 0.8070 (p0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2220 time to fit residues: 45.8176 Evaluate side-chains 102 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 51.1168 > 50: distance: 23 - 40: 17.968 distance: 36 - 40: 16.212 distance: 40 - 41: 9.203 distance: 41 - 42: 16.151 distance: 41 - 44: 13.975 distance: 42 - 43: 25.327 distance: 42 - 46: 10.580 distance: 44 - 45: 22.550 distance: 46 - 47: 8.630 distance: 47 - 48: 26.734 distance: 47 - 50: 23.201 distance: 48 - 49: 22.213 distance: 48 - 52: 6.602 distance: 50 - 51: 29.073 distance: 52 - 53: 8.453 distance: 53 - 54: 10.439 distance: 53 - 56: 8.485 distance: 54 - 55: 7.714 distance: 54 - 58: 15.569 distance: 56 - 57: 25.616 distance: 59 - 60: 4.544 distance: 59 - 62: 21.115 distance: 60 - 61: 12.000 distance: 60 - 65: 10.354 distance: 62 - 63: 27.674 distance: 62 - 64: 21.206 distance: 65 - 66: 17.769 distance: 66 - 67: 30.033 distance: 66 - 69: 12.026 distance: 67 - 68: 14.734 distance: 67 - 76: 6.361 distance: 69 - 70: 26.195 distance: 70 - 71: 17.890 distance: 70 - 72: 17.394 distance: 71 - 73: 27.799 distance: 72 - 74: 11.793 distance: 73 - 75: 27.627 distance: 74 - 75: 18.077 distance: 76 - 77: 19.171 distance: 77 - 78: 16.036 distance: 77 - 80: 17.988 distance: 78 - 79: 12.721 distance: 78 - 87: 8.218 distance: 80 - 81: 15.811 distance: 81 - 82: 16.844 distance: 81 - 83: 34.469 distance: 84 - 86: 39.077 distance: 85 - 86: 14.818 distance: 87 - 88: 14.184 distance: 88 - 89: 10.196 distance: 88 - 91: 19.793 distance: 89 - 90: 7.568 distance: 89 - 94: 7.963 distance: 91 - 92: 18.059 distance: 91 - 93: 9.495 distance: 94 - 95: 10.719 distance: 95 - 96: 10.659 distance: 95 - 98: 13.272 distance: 96 - 97: 11.497 distance: 96 - 101: 13.544 distance: 98 - 99: 10.604 distance: 98 - 100: 8.967 distance: 101 - 102: 7.484 distance: 102 - 103: 6.504 distance: 102 - 105: 9.285 distance: 103 - 104: 13.101 distance: 103 - 107: 17.332 distance: 105 - 106: 19.562 distance: 107 - 108: 11.060 distance: 108 - 109: 23.613 distance: 108 - 111: 15.398 distance: 109 - 110: 22.142 distance: 109 - 113: 3.726 distance: 111 - 112: 17.474