Starting phenix.real_space_refine on Sat Dec 16 12:32:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/12_2023/6n2y_9333_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/12_2023/6n2y_9333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/12_2023/6n2y_9333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/12_2023/6n2y_9333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/12_2023/6n2y_9333_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/12_2023/6n2y_9333_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.229 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 12 5.49 5 Mg 4 5.21 5 S 98 5.16 5 C 22291 2.51 5 N 6106 2.21 5 O 6532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "B ARG 4": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 171": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "C ARG 140": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D ARG 435": "NH1" <-> "NH2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 240": "NH1" <-> "NH2" Residue "E ARG 333": "NH1" <-> "NH2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 404": "NH1" <-> "NH2" Residue "F ARG 5": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 120": "NH1" <-> "NH2" Residue "F ARG 240": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "G ARG 5": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 102": "NH1" <-> "NH2" Residue "I ARG 9": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "b2 ARG 40": "NH1" <-> "NH2" Residue "b1 ARG 40": "NH1" <-> "NH2" Residue "a ARG 39": "NH1" <-> "NH2" Residue "a ARG 74": "NH1" <-> "NH2" Residue "c0 ARG 36": "NH1" <-> "NH2" Residue "c2 ARG 36": "NH1" <-> "NH2" Residue "c3 ARG 36": "NH1" <-> "NH2" Residue "c3 ARG 72": "NH1" <-> "NH2" Residue "c4 ARG 36": "NH1" <-> "NH2" Residue "c5 ARG 36": "NH1" <-> "NH2" Residue "c6 ARG 36": "NH1" <-> "NH2" Residue "c7 ARG 36": "NH1" <-> "NH2" Residue "c8 ARG 29": "NH1" <-> "NH2" Residue "c8 ARG 36": "NH1" <-> "NH2" Residue "c9 ARG 36": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 35043 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3827 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3787 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 476} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3766 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 470} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3593 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3621 Classifications: {'peptide': 471} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2187 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 928 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 122} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "I" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1284 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "b2" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 854 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 1, 'TRANS': 149} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 11, 'ASN:plan1': 2, 'UNK:plan-1': 17, 'ASP:plan': 1, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 204 Chain: "b1" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 889 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 1, 'TRANS': 155} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 310 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 14, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 27, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 238 Chain: "a" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1486 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "c0" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c1" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c2" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c3" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c4" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c5" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c6" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c7" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c8" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "c9" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 507 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "A" 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: "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: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.43, per 1000 atoms: 0.55 Number of scatterers: 35043 At special positions: 0 Unit cell: (128.26, 137.8, 227.9, 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 98 16.00 P 12 15.00 Mg 4 11.99 O 6532 8.00 N 6106 7.00 C 22291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.92 Conformation dependent library (CDL) restraints added in 6.5 seconds 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8582 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 27 sheets defined 53.5% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 3.551A pdb=" N GLN A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 175 through 187 removed outlier: 4.276A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 232 through 251 Proline residue: A 239 - end of helix removed outlier: 4.192A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 4.500A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.778A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 419 removed outlier: 3.630A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.603A pdb=" N VAL A 453 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 459 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 461 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.643A pdb=" N LYS A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 19 removed outlier: 3.617A pdb=" N TYR B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.591A pdb=" N ASN B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 238 through 251 removed outlier: 4.151A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.074A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 293 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 298 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 375 through 395 removed outlier: 4.651A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 4.346A pdb=" N GLN B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 407' Processing helix chain 'B' and resid 410 through 420 removed outlier: 4.310A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 466 removed outlier: 3.702A pdb=" N VAL B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 459 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B 465 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 466 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.910A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.561A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 238 through 252 removed outlier: 3.996A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 288 through 298 removed outlier: 4.469A pdb=" N PHE C 291 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 292 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 296 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 373 through 395 removed outlier: 3.568A pdb=" N LYS C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 419 Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.765A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 3.748A pdb=" N VAL C 453 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU C 459 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN C 466 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 486 through 497 removed outlier: 3.610A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 164 through 178 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 243 removed outlier: 5.098A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.622A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 281 through 289 removed outlier: 3.703A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 324 removed outlier: 4.033A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 361 through 379 removed outlier: 3.622A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 Processing helix chain 'D' and resid 396 through 409 Processing helix chain 'D' and resid 418 through 421 No H-bonds generated for 'chain 'D' and resid 418 through 421' Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 459 through 468 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 204 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.178A pdb=" N ARG E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET E 235 " --> pdb=" O THR E 231 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 268 Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 281 through 289 Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 321 Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 361 through 386 removed outlier: 4.571A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 409 removed outlier: 4.169A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.729A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR E 421 " --> pdb=" O GLU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 461 through 469 Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 144 Processing helix chain 'F' and resid 164 through 175 Processing helix chain 'F' and resid 192 through 205 WARNING: missing atoms! Processing helix chain 'F' and resid 222 through 242 removed outlier: 3.880A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.561A pdb=" N GLN F 259 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU F 263 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER F 265 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 276 No H-bonds generated for 'chain 'F' and resid 274 through 276' Processing helix chain 'F' and resid 283 through 291 removed outlier: 3.554A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 319 No H-bonds generated for 'chain 'F' and resid 316 through 319' Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 361 through 378 Processing helix chain 'F' and resid 381 through 386 Processing helix chain 'F' and resid 396 through 409 removed outlier: 3.754A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 418 No H-bonds generated for 'chain 'F' and resid 416 through 418' Processing helix chain 'F' and resid 430 through 441 Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 459 through 469 Processing helix chain 'G' and resid 4 through 57 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 91 through 106 removed outlier: 4.078A pdb=" N ARG G 106 " --> pdb=" O THR G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 147 through 161 removed outlier: 4.222A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 282 Proline residue: G 218 - end of helix Processing helix chain 'H' and resid 88 through 130 removed outlier: 3.942A pdb=" N ALA H 95 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU H 98 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP H 112 " --> pdb=" O ASP H 109 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG H 115 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG H 126 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL H 129 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 21 Processing helix chain 'I' and resid 24 through 40 Processing helix chain 'I' and resid 43 through 48 Processing helix chain 'I' and resid 55 through 65 Processing helix chain 'I' and resid 71 through 82 Processing helix chain 'I' and resid 86 through 104 removed outlier: 3.756A pdb=" N VAL I 89 " --> pdb=" O PHE I 86 " (cutoff:3.500A) Proline residue: I 90 - end of helix removed outlier: 4.034A pdb=" N ASP I 101 " --> pdb=" O ALA I 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG I 104 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 133 removed outlier: 3.586A pdb=" N ARG I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN I 131 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS I 132 " --> pdb=" O VAL I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 175 Processing helix chain 'b2' and resid 11 through 122 removed outlier: 5.288A pdb=" N GLNb2 31 " --> pdb=" O LYSb2 27 " (cutoff:3.500A) Proline residue: b2 32 - end of helix removed outlier: 3.518A pdb=" N ILEb2 44 " --> pdb=" O ARGb2 40 " (cutoff:3.500A) Processing helix chain 'b2' and resid 125 through 139 removed outlier: 3.534A pdb=" N ALAb2 129 " --> pdb=" O ARGb2 125 " (cutoff:3.500A) Processing helix chain 'b2' and resid 601 through 615 Processing helix chain 'b1' and resid 10 through 142 removed outlier: 3.620A pdb=" N TRPb1 30 " --> pdb=" O ARGb1 26 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLNb1 31 " --> pdb=" O LYSb1 27 " (cutoff:3.500A) Proline residue: b1 32 - end of helix removed outlier: 3.958A pdb=" N ALAb1 51 " --> pdb=" O GLUb1 47 " (cutoff:3.500A) Processing helix chain 'b1' and resid 146 through 162 Processing helix chain 'a' and resid 17 through 37 Processing helix chain 'a' and resid 49 through 66 Processing helix chain 'a' and resid 69 through 72 No H-bonds generated for 'chain 'a' and resid 69 through 72' Processing helix chain 'a' and resid 74 through 95 removed outlier: 4.057A pdb=" N THR a 77 " --> pdb=" O ARG a 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY a 79 " --> pdb=" O LEU a 76 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL a 80 " --> pdb=" O THR a 77 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR a 81 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE a 83 " --> pdb=" O VAL a 80 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET a 84 " --> pdb=" O THR a 81 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL a 86 " --> pdb=" O ILE a 83 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL a 88 " --> pdb=" O TYR a 85 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU a 92 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY a 93 " --> pdb=" O ASN a 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU a 94 " --> pdb=" O MET a 91 " (cutoff:3.500A) Proline residue: a 95 - end of helix Processing helix chain 'a' and resid 113 through 129 Processing helix chain 'a' and resid 153 through 190 removed outlier: 4.630A pdb=" N GLY a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 200 through 233 Processing helix chain 'c0' and resid 3 through 36 Processing helix chain 'c0' and resid 38 through 71 removed outlier: 3.834A pdb=" N ARGc0 41 " --> pdb=" O PROc0 38 " (cutoff:3.500A) Proline residue: c0 42 - end of helix removed outlier: 4.381A pdb=" N THRc0 46 " --> pdb=" O VALc0 43 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THRc0 47 " --> pdb=" O LEUc0 44 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VALc0 55 " --> pdb=" O VALc0 52 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLUc0 56 " --> pdb=" O ALAc0 53 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEUc0 58 " --> pdb=" O VALc0 55 " (cutoff:3.500A) Proline residue: c0 59 - end of helix removed outlier: 3.506A pdb=" N PHEc0 67 " --> pdb=" O VALc0 64 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLYc0 71 " --> pdb=" O ILEc0 68 " (cutoff:3.500A) Processing helix chain 'c1' and resid 3 through 36 Processing helix chain 'c1' and resid 38 through 55 removed outlier: 3.523A pdb=" N ARGc1 41 " --> pdb=" O PROc1 38 " (cutoff:3.500A) Proline residue: c1 42 - end of helix removed outlier: 3.696A pdb=" N THRc1 47 " --> pdb=" O LEUc1 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEc1 50 " --> pdb=" O THRc1 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALAc1 53 " --> pdb=" O ILEc1 50 " (cutoff:3.500A) Processing helix chain 'c1' and resid 57 through 71 Processing helix chain 'c2' and resid 3 through 36 Processing helix chain 'c2' and resid 38 through 71 removed outlier: 3.781A pdb=" N ARGc2 41 " --> pdb=" O PROc2 38 " (cutoff:3.500A) Proline residue: c2 42 - end of helix removed outlier: 3.518A pdb=" N THRc2 47 " --> pdb=" O LEUc2 44 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALAc2 57 " --> pdb=" O LEUc2 54 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEUc2 58 " --> pdb=" O VALc2 55 " (cutoff:3.500A) Proline residue: c2 59 - end of helix Processing helix chain 'c3' and resid 3 through 36 Processing helix chain 'c3' and resid 38 through 71 removed outlier: 3.973A pdb=" N ARGc3 41 " --> pdb=" O PROc3 38 " (cutoff:3.500A) Proline residue: c3 42 - end of helix removed outlier: 3.513A pdb=" N THRc3 47 " --> pdb=" O LEUc3 44 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N METc3 48 " --> pdb=" O GLNc3 45 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALc3 52 " --> pdb=" O PHEc3 49 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLUc3 56 " --> pdb=" O ALAc3 53 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEUc3 58 " --> pdb=" O VALc3 55 " (cutoff:3.500A) Proline residue: c3 59 - end of helix removed outlier: 3.829A pdb=" N GLYc3 71 " --> pdb=" O ILEc3 68 " (cutoff:3.500A) Processing helix chain 'c4' and resid 4 through 36 Processing helix chain 'c4' and resid 38 through 71 removed outlier: 3.597A pdb=" N ARGc4 41 " --> pdb=" O PROc4 38 " (cutoff:3.500A) Proline residue: c4 42 - end of helix removed outlier: 3.602A pdb=" N THRc4 47 " --> pdb=" O LEUc4 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILEc4 50 " --> pdb=" O THRc4 47 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALAc4 53 " --> pdb=" O ILEc4 50 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALAc4 57 " --> pdb=" O LEUc4 54 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEUc4 58 " --> pdb=" O VALc4 55 " (cutoff:3.500A) Proline residue: c4 59 - end of helix removed outlier: 3.977A pdb=" N PHEc4 67 " --> pdb=" O VALc4 64 " (cutoff:3.500A) Processing helix chain 'c5' and resid 4 through 36 Processing helix chain 'c5' and resid 41 through 71 removed outlier: 4.290A pdb=" N LEUc5 58 " --> pdb=" O LEUc5 54 " (cutoff:3.500A) Proline residue: c5 59 - end of helix Processing helix chain 'c6' and resid 4 through 36 Processing helix chain 'c6' and resid 41 through 71 removed outlier: 4.372A pdb=" N LEUc6 58 " --> pdb=" O LEUc6 54 " (cutoff:3.500A) Proline residue: c6 59 - end of helix removed outlier: 3.635A pdb=" N GLYc6 71 " --> pdb=" O PHEc6 67 " (cutoff:3.500A) Processing helix chain 'c7' and resid 3 through 36 Processing helix chain 'c7' and resid 38 through 71 Proline residue: c7 42 - end of helix removed outlier: 3.633A pdb=" N THRc7 47 " --> pdb=" O LEUc7 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLUc7 56 " --> pdb=" O ALAc7 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALAc7 57 " --> pdb=" O LEUc7 54 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEUc7 58 " --> pdb=" O VALc7 55 " (cutoff:3.500A) Proline residue: c7 59 - end of helix removed outlier: 3.510A pdb=" N LEUc7 70 " --> pdb=" O PHEc7 67 " (cutoff:3.500A) Processing helix chain 'c8' and resid 4 through 36 Processing helix chain 'c8' and resid 38 through 71 Proline residue: c8 42 - end of helix removed outlier: 3.614A pdb=" N THRc8 47 " --> pdb=" O LEUc8 44 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILEc8 50 " --> pdb=" O THRc8 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALAc8 53 " --> pdb=" O ILEc8 50 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLUc8 56 " --> pdb=" O ALAc8 53 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALAc8 57 " --> pdb=" O LEUc8 54 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUc8 58 " --> pdb=" O VALc8 55 " (cutoff:3.500A) Proline residue: c8 59 - end of helix removed outlier: 3.965A pdb=" N GLYc8 71 " --> pdb=" O ILEc8 68 " (cutoff:3.500A) Processing helix chain 'c9' and resid 4 through 36 Processing helix chain 'c9' and resid 41 through 70 removed outlier: 3.827A pdb=" N THRc9 47 " --> pdb=" O VALc9 43 " (cutoff:3.500A) Proline residue: c9 59 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 41 through 43 removed outlier: 3.890A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.682A pdb=" N ARG A 127 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.828A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 169 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 8.544A pdb=" N ILE A 222 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS A 255 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE A 194 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 257 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 196 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL A 259 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 198 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP A 261 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 4.313A pdb=" N MET B 60 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.000A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 340 through 344 removed outlier: 3.502A pdb=" N VAL B 319 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.700A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 31 through 35 removed outlier: 6.399A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.409A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.641A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 319 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 221 through 226 removed outlier: 8.667A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP C 261 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 29 through 34 removed outlier: 6.410A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 302 through 305 removed outlier: 7.124A pdb=" N ALA D 327 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE D 157 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR D 329 " --> pdb=" O PHE D 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 211 through 216 removed outlier: 6.816A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL D 184 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 248 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA D 186 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE D 250 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 188 " --> pdb=" O PHE D 250 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASP D 252 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER D 299 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU D 249 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR D 301 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE D 251 " --> pdb=" O THR D 301 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.661A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= S, first strand: chain 'E' and resid 327 through 330 removed outlier: 8.423A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 188 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 5 through 10 removed outlier: 6.318A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= V, first strand: chain 'F' and resid 94 through 96 removed outlier: 4.166A pdb=" N ARG F 94 " --> pdb=" O THR F 211 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA F 327 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE F 157 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR F 329 " --> pdb=" O PHE F 157 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 133 through 135 removed outlier: 4.632A pdb=" N GLU F 133 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 113 through 118 removed outlier: 6.362A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 189 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 5 through 9 Processing sheet with id= Z, first strand: chain 'H' and resid 48 through 52 removed outlier: 3.629A pdb=" N SER H 48 " --> pdb=" O VAL H 63 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 137 through 143 removed outlier: 3.999A pdb=" N SER I 113 " --> pdb=" O ILE I 143 " (cutoff:3.500A) 1883 hydrogen bonds defined for protein. 4956 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: 11.76 Time building geometry restraints manager: 15.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5932 1.30 - 1.43: 8273 1.43 - 1.56: 21039 1.56 - 1.68: 139 1.68 - 1.81: 195 Bond restraints: 35578 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" CA GLUb1 75 " pdb=" CB GLUb1 75 " ideal model delta sigma weight residual 1.528 1.655 -0.127 1.56e-02 4.11e+03 6.60e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" CA LEUb2 131 " pdb=" CB LEUb2 131 " ideal model delta sigma weight residual 1.528 1.656 -0.127 1.59e-02 3.96e+03 6.40e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 ... (remaining 35573 not shown) Histogram of bond angle deviations from ideal: 96.10 - 104.16: 558 104.16 - 112.23: 17310 112.23 - 120.30: 16787 120.30 - 128.37: 13482 128.37 - 136.44: 196 Bond angle restraints: 48333 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 122.36 17.51 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 121.10 15.73 1.00e+00 1.00e+00 2.47e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 125.97 13.90 1.00e+00 1.00e+00 1.93e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 123.73 13.10 1.00e+00 1.00e+00 1.72e+02 ... (remaining 48328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.32: 20893 23.32 - 46.65: 552 46.65 - 69.97: 25 69.97 - 93.30: 29 93.30 - 116.62: 1 Dihedral angle restraints: 21500 sinusoidal: 8114 harmonic: 13386 Sorted by residual: dihedral pdb=" C ARGb1 99 " pdb=" N ARGb1 99 " pdb=" CA ARGb1 99 " pdb=" CB ARGb1 99 " ideal model delta harmonic sigma weight residual -122.60 -138.06 15.46 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" N ARGb1 99 " pdb=" C ARGb1 99 " pdb=" CA ARGb1 99 " pdb=" CB ARGb1 99 " ideal model delta harmonic sigma weight residual 122.80 138.26 -15.46 0 2.50e+00 1.60e-01 3.82e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 -176.62 116.62 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 21497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 5534 0.141 - 0.283: 215 0.283 - 0.424: 31 0.424 - 0.565: 6 0.565 - 0.707: 2 Chirality restraints: 5788 Sorted by residual: chirality pdb=" CA ARGb1 99 " pdb=" N ARGb1 99 " pdb=" C ARGb1 99 " pdb=" CB ARGb1 99 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.25e+01 chirality pdb=" CA GLNb2 90 " pdb=" N GLNb2 90 " pdb=" C GLNb2 90 " pdb=" CB GLNb2 90 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ILEb1 157 " pdb=" N ILEb1 157 " pdb=" C ILEb1 157 " pdb=" CB ILEb1 157 " both_signs ideal model delta sigma weight residual False 2.43 1.88 0.55 2.00e-01 2.50e+01 7.52e+00 ... (remaining 5785 not shown) Planarity restraints: 6254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEUb1 144 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEUb1 144 " 0.079 2.00e-02 2.50e+03 pdb=" O LEUb1 144 " -0.032 2.00e-02 2.50e+03 pdb=" N THRb1 145 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLNb1 127 " 0.019 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C GLNb1 127 " -0.069 2.00e-02 2.50e+03 pdb=" O GLNb1 127 " 0.025 2.00e-02 2.50e+03 pdb=" N VALb1 128 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLUb1 64 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C GLUb1 64 " 0.065 2.00e-02 2.50e+03 pdb=" O GLUb1 64 " -0.025 2.00e-02 2.50e+03 pdb=" N GLNb1 65 " -0.022 2.00e-02 2.50e+03 ... (remaining 6251 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.59: 5 1.59 - 2.42: 91 2.42 - 3.25: 34448 3.25 - 4.07: 91966 4.07 - 4.90: 167696 Warning: very small nonbonded interaction distances. Nonbonded interactions: 294206 Sorted by model distance: nonbonded pdb=" O PRO H 36 " pdb=" OE2 GLUc5 39 " model vdw 0.765 3.040 nonbonded pdb=" N LEU H 32 " pdb=" NE2 GLNc4 37 " model vdw 1.152 3.200 nonbonded pdb=" O PRO H 36 " pdb=" CD GLUc5 39 " model vdw 1.382 3.270 nonbonded pdb=" CA LEU H 32 " pdb=" NE2 GLNc4 37 " model vdw 1.441 3.550 nonbonded pdb=" O ASNb1 46 " pdb=" OD1 ASPb1 49 " model vdw 1.500 3.040 ... (remaining 294201 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 8 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (nam \ e N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 and (n \ ame N or name CA or name C or name O or name CB )) or resid 20 through 187 or (r \ esid 188 and (name N or name CA or name C or name O or name CB )) or resid 189 t \ hrough 352 or (resid 353 and (name N or name CA or name C or name CB or name CG1 \ or name CG2)) or resid 354 through 394 or (resid 395 through 398 and (name N or \ name CA or name C or name O or name CB )) or resid 399 through 405 or (resid 40 \ 6 through 408 and (name N or name CA or name C or name O or name CB )) or resid \ 409 through 483 or (resid 484 through 485 and (name N or name CA or name C or na \ me O or name CB )) or resid 486 through 495 or (resid 496 and (name N or name CA \ or name C or name O or name CB )) or resid 497 through 501 or resid 600 through \ 601)) selection = (chain 'B' and (resid 8 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 16 or (resid 17 and (nam \ e N or name CA or name C or name O or name CB )) or resid 18 or (resid 19 and (n \ ame N or name CA or name C or name O or name CB )) or resid 20 through 38 or (re \ sid 39 and (name N or name CA or name C or name CB )) or resid 40 through 187 or \ (resid 188 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 9 through 393 or (resid 394 and (name N or name CA or name C or name CB )) or re \ sid 395 through 501 or resid 600 through 601)) selection = (chain 'C' and (resid 8 through 38 or (resid 39 and (name N or name CA or name C \ or name CB )) or resid 40 through 352 or (resid 353 and (name N or name CA or n \ ame C or name CB or name CG1 or name CG2)) or resid 354 through 393 or (resid 39 \ 4 and (name N or name CA or name C or name CB )) or (resid 395 through 398 and ( \ name N or name CA or name C or name O or name CB )) or resid 399 through 402 or \ (resid 403 through 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 450 or (resid 451 and (name N or name CA or name C or name \ O or name CB )) or resid 452 through 483 or (resid 484 through 485 and (name N o \ r name CA or name C or name O or name CB )) or resid 486 through 495 or (resid 4 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 497 through \ 501 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name ND2)) or resid 197 through 208 or ( \ resid 209 and (name N or name CA or name C or name CB or name OG )) or resid 210 \ through 296 or (resid 297 and (name N or name CA or name C or name CB or name C \ G or name CD or name CE or name NZ )) or resid 298 through 385 or (resid 386 and \ (name N or name CA or name C or name O or name CB )) or resid 387 through 388 o \ r (resid 389 through 392 and (name N or name CA or name C or name O or name CB ) \ ) or resid 393 or (resid 394 through 395 and (name N or name CA or name C or nam \ e O or name CB )) or resid 396 or (resid 397 and (name N or name CA or name C or \ name O or name CB )) or resid 398 through 420 or (resid 421 and (name N or name \ CA or name C or name CB or name OG1 or name CG2)) or (resid 422 and (name N or \ name CA or name C )) or resid 423 through 430 or (resid 431 and (name N or name \ CA or name C or name O or name CB )) or resid 432 through 468 or (resid 469 and \ (name N or name CA or name C or name O or name CB )) or resid 470)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name CB or name CG or name OD1 or name ND2)) or resid 197 through 208 or ( \ resid 209 and (name N or name CA or name C or name CB or name OG )) or resid 210 \ through 296 or (resid 297 and (name N or name CA or name C or name CB or name C \ G or name CD or name CE or name NZ )) or resid 298 through 420 or (resid 421 and \ (name N or name CA or name C or name CB or name OG1 or name CG2)) or (resid 422 \ and (name N or name CA or name C )) or resid 423 through 430 or (resid 431 and \ (name N or name CA or name C or name O or name CB )) or resid 432 through 470)) selection = (chain 'F' and (resid 2 through 385 or (resid 386 and (name N or name CA or name \ C or name O or name CB )) or resid 387 through 388 or (resid 389 through 392 an \ d (name N or name CA or name C or name O or name CB )) or resid 393 or (resid 39 \ 4 through 395 and (name N or name CA or name C or name O or name CB )) or resid \ 396 or (resid 397 and (name N or name CA or name C or name O or name CB )) or re \ sid 398 through 468 or (resid 469 and (name N or name CA or name C or name O or \ name CB )) or resid 470)) } ncs_group { reference = (chain 'b1' and ((resid 7 and (name N or name CA or name C or name O or name CB \ )) or resid 8 through 19 or (resid 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43 or (resid 44 through 139 and \ (name N or name CA or name C or name O or name CB )) or (resid 140 and (name N o \ r name CA or name C or name CB )))) selection = (chain 'b2' and (resid 7 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 33 or (resid 34 and ( \ name N or name CA or name C or name O or name CB )) or resid 35 through 140)) } ncs_group { reference = chain 'c0' selection = chain 'c1' selection = chain 'c2' selection = chain 'c3' selection = chain 'c4' selection = chain 'c5' selection = chain 'c6' selection = chain 'c7' selection = chain 'c8' selection = chain 'c9' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.030 Extract box with map and model: 8.510 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 94.390 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.280 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:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 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 : 0.009 0.127 35578 Z= 0.598 Angle : 1.188 17.851 48333 Z= 0.733 Chirality : 0.072 0.707 5788 Planarity : 0.008 0.077 6254 Dihedral : 10.710 116.619 12918 Min Nonbonded Distance : 0.765 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.38 % Favored : 96.49 % Rotamer: Outliers : 0.40 % Allowed : 5.43 % Favored : 94.17 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 3.57 % 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: -2.50 (0.11), residues: 4648 helix: -1.55 (0.09), residues: 2510 sheet: -1.02 (0.22), residues: 508 loop : -1.74 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 206 HIS 0.027 0.002 HIS F 363 PHE 0.043 0.003 PHEc6 65 TYR 0.045 0.003 TYR C 329 ARG 0.021 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 780 time to evaluate : 3.930 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash 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: 14 outliers final: 4 residues processed: 793 average time/residue: 1.5795 time to fit residues: 1486.4974 Evaluate side-chains 501 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 497 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 5.0144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 10.0000 chunk 353 optimal weight: 50.0000 chunk 196 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 238 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 424 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 113 GLN A 147 GLN A 186 GLN A 215 HIS A 358 ASN A 422 GLN A 425 HIS B 46 ASN B 57 ASN B 147 GLN B 186 GLN B 215 HIS B 322 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS C 18 ASN C 186 GLN C 215 HIS C 333 ASN C 345 GLN C 397 GLN C 422 GLN C 425 HIS ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN D 34 HIS D 169 GLN D 179 HIS D 217 GLN D 289 GLN D 304 GLN D 324 HIS ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 289 GLN E 304 GLN E 375 GLN E 381 GLN E 415 HIS F 28 ASN F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 GLN G 33 ASN G 50 GLN G 94 ASN G 130 ASN G 282 ASN I 16 GLN a 16 ASN a 128 HIS ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 HIS ** c1 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c4 37 GLN c5 23 ASN c7 23 ASN c7 37 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35578 Z= 0.236 Angle : 0.636 9.816 48333 Z= 0.325 Chirality : 0.045 0.213 5788 Planarity : 0.006 0.058 6254 Dihedral : 6.430 78.953 5171 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 3.51 % Allowed : 12.66 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.84 (0.12), residues: 4648 helix: -0.01 (0.10), residues: 2506 sheet: -0.66 (0.22), residues: 542 loop : -1.21 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 206 HIS 0.010 0.001 HIS E 363 PHE 0.024 0.001 PHE A 456 TYR 0.043 0.002 TYRc6 69 ARG 0.007 0.001 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 523 time to evaluate : 4.430 Fit side-chains TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 123 outliers final: 41 residues processed: 607 average time/residue: 1.3660 time to fit residues: 1010.7140 Evaluate side-chains 503 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 462 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 26 residues processed: 15 average time/residue: 0.9989 time to fit residues: 24.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 352 optimal weight: 9.9990 chunk 288 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 424 optimal weight: 5.9990 chunk 458 optimal weight: 6.9990 chunk 378 optimal weight: 20.0000 chunk 421 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 chunk 340 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS B 426 GLN D 22 HIS D 169 GLN D 289 GLN D 304 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 200 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 130 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35578 Z= 0.204 Angle : 0.609 17.635 48333 Z= 0.303 Chirality : 0.044 0.282 5788 Planarity : 0.005 0.058 6254 Dihedral : 6.064 86.866 5171 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 3.46 % Allowed : 14.20 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.16 (0.12), residues: 4648 helix: 0.58 (0.10), residues: 2498 sheet: -0.47 (0.22), residues: 550 loop : -0.92 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 105 HIS 0.008 0.001 HIS E 363 PHE 0.033 0.001 PHE a 209 TYR 0.029 0.001 TYRc6 69 ARG 0.005 0.000 ARGb2 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 494 time to evaluate : 4.199 Fit side-chains TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 121 outliers final: 55 residues processed: 572 average time/residue: 1.3939 time to fit residues: 969.4459 Evaluate side-chains 510 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 455 time to evaluate : 3.951 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 39 residues processed: 19 average time/residue: 0.5090 time to fit residues: 20.5137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 220 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 426 optimal weight: 5.9990 chunk 451 optimal weight: 20.0000 chunk 222 optimal weight: 0.6980 chunk 404 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 ASN B 46 ASN C 422 GLN ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN E 401 HIS F 28 ASN F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN F 401 HIS G 130 ASN I 41 ASN ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c7 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 35578 Z= 0.533 Angle : 0.735 12.678 48333 Z= 0.372 Chirality : 0.051 0.305 5788 Planarity : 0.006 0.059 6254 Dihedral : 6.519 87.220 5171 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.92 % Favored : 96.04 % Rotamer: Outliers : 4.66 % Allowed : 14.54 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.23 (0.12), residues: 4648 helix: 0.54 (0.10), residues: 2506 sheet: -0.69 (0.21), residues: 556 loop : -0.89 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 206 HIS 0.015 0.002 HIS E 363 PHE 0.026 0.002 PHE a 160 TYR 0.027 0.002 TYR E 364 ARG 0.014 0.001 ARGb1 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 472 time to evaluate : 3.975 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 outliers start: 163 outliers final: 88 residues processed: 596 average time/residue: 1.4412 time to fit residues: 1039.4493 Evaluate side-chains 536 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 448 time to evaluate : 4.344 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 68 residues processed: 24 average time/residue: 0.7780 time to fit residues: 32.1290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 50.0000 chunk 256 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 336 optimal weight: 0.0070 chunk 186 optimal weight: 0.8980 chunk 385 optimal weight: 50.0000 chunk 312 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 405 optimal weight: 30.0000 chunk 113 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS B 172 GLN B 189 GLN B 470 HIS ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 90 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35578 Z= 0.199 Angle : 0.598 16.562 48333 Z= 0.299 Chirality : 0.044 0.298 5788 Planarity : 0.004 0.059 6254 Dihedral : 6.024 78.914 5171 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 4.23 % Allowed : 16.17 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.24 (0.12), residues: 4648 helix: 0.91 (0.11), residues: 2496 sheet: -0.56 (0.21), residues: 573 loop : -0.64 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 206 HIS 0.006 0.001 HIS E 363 PHE 0.024 0.001 PHE a 171 TYR 0.024 0.001 TYR B 438 ARG 0.008 0.000 ARG E 435 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 477 time to evaluate : 4.087 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 148 outliers final: 79 residues processed: 588 average time/residue: 1.4771 time to fit residues: 1056.6196 Evaluate side-chains 520 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 441 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 67 residues processed: 14 average time/residue: 0.7583 time to fit residues: 20.4478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 1.9990 chunk 406 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 265 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 451 optimal weight: 4.9990 chunk 375 optimal weight: 30.0000 chunk 209 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 237 optimal weight: 0.0570 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 28 ASN D 289 GLN D 304 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35578 Z= 0.258 Angle : 0.617 17.925 48333 Z= 0.307 Chirality : 0.045 0.282 5788 Planarity : 0.005 0.060 6254 Dihedral : 6.008 80.209 5171 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 3.51 % Allowed : 17.49 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.36 (0.12), residues: 4648 helix: 0.98 (0.11), residues: 2501 sheet: -0.47 (0.22), residues: 554 loop : -0.54 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 206 HIS 0.007 0.001 HIS E 363 PHE 0.020 0.001 PHE a 160 TYR 0.018 0.001 TYR B 438 ARG 0.013 0.000 ARGb2 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9296 Ramachandran restraints generated. 4648 Oldfield, 0 Emsley, 4648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 454 time to evaluate : 3.957 Fit side-chains TARDY: cannot create tardy model for: "THR F 421 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 123 outliers final: 79 residues processed: 545 average time/residue: 1.2836 time to fit residues: 847.8379 Evaluate side-chains 514 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 435 time to evaluate : 2.927 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 65 residues processed: 16 average time/residue: 0.3598 time to fit residues: 13.3461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 257 optimal weight: 0.8980 chunk 329 optimal weight: 0.8980 chunk 255 optimal weight: 0.3980 chunk 380 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 450 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 274 optimal weight: 0.0970 chunk 207 optimal weight: 0.0170 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: