Starting phenix.real_space_refine on Sat Mar 23 00:44:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/03_2024/6n2y_9333_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/03_2024/6n2y_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_9333/03_2024/6n2y_9333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/03_2024/6n2y_9333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/03_2024/6n2y_9333_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n2y_9333/03_2024/6n2y_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-dev-5265/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: 17.89, per 1000 atoms: 0.51 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: 14.03 Conformation dependent library (CDL) restraints added in 6.7 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: 6.68 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: 12.20 Time building geometry restraints manager: 15.19 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: 1.770 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: 8.420 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 90.910 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.070 ------------------------------------------------------------------------------- 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 : 3.767 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: A 11 LEU cc_start: 0.8170 (mt) cc_final: 0.7969 (mp) REVERT: A 214 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8142 (tttp) REVERT: A 250 MET cc_start: 0.8756 (ttp) cc_final: 0.8314 (ttp) REVERT: A 252 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8426 (mtpp) REVERT: A 262 ASP cc_start: 0.7469 (m-30) cc_final: 0.7121 (m-30) REVERT: A 347 ASP cc_start: 0.7443 (m-30) cc_final: 0.7179 (m-30) REVERT: A 373 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7973 (ttpp) REVERT: A 385 ASP cc_start: 0.7847 (m-30) cc_final: 0.7533 (m-30) REVERT: A 458 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7804 (tttp) REVERT: A 489 LYS cc_start: 0.8337 (mtmt) cc_final: 0.8097 (mtmt) REVERT: B 28 VAL cc_start: 0.8942 (t) cc_final: 0.8625 (p) REVERT: B 214 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8285 (mtmm) REVERT: C 95 MET cc_start: 0.8381 (tpt) cc_final: 0.7896 (tpt) REVERT: C 250 MET cc_start: 0.9070 (ttp) cc_final: 0.8732 (ttm) REVERT: C 262 ASP cc_start: 0.7547 (m-30) cc_final: 0.7248 (m-30) REVERT: C 465 ASP cc_start: 0.7514 (m-30) cc_final: 0.7300 (m-30) REVERT: C 467 ASN cc_start: 0.7244 (m-40) cc_final: 0.6881 (m110) REVERT: D 75 GLU cc_start: 0.7717 (tt0) cc_final: 0.7237 (tm-30) REVERT: D 98 VAL cc_start: 0.8807 (t) cc_final: 0.8591 (p) REVERT: D 332 GLU cc_start: 0.7506 (tp30) cc_final: 0.7265 (tp30) REVERT: D 381 GLN cc_start: 0.7929 (tt0) cc_final: 0.6929 (tp40) REVERT: D 431 LYS cc_start: 0.7624 (mtpm) cc_final: 0.7370 (mtpp) REVERT: D 467 LYS cc_start: 0.7622 (mtmt) cc_final: 0.6882 (mptt) REVERT: E 39 GLU cc_start: 0.7959 (pm20) cc_final: 0.7746 (pm20) REVERT: E 90 VAL cc_start: 0.8593 (m) cc_final: 0.8342 (p) REVERT: E 375 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7506 (tp40) REVERT: E 427 TYR cc_start: 0.8740 (t80) cc_final: 0.8460 (t80) REVERT: F 30 LEU cc_start: 0.8791 (mt) cc_final: 0.8556 (mp) REVERT: F 281 LEU cc_start: 0.8806 (tm) cc_final: 0.8590 (tp) REVERT: F 337 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8190 (mt-10) REVERT: F 438 LYS cc_start: 0.7967 (tttt) cc_final: 0.7655 (ttpp) REVERT: G 8 LYS cc_start: 0.8216 (tptt) cc_final: 0.7962 (tptt) REVERT: G 15 LYS cc_start: 0.8234 (mttt) cc_final: 0.7920 (mttm) REVERT: G 40 LYS cc_start: 0.7982 (mtpm) cc_final: 0.7559 (ttpp) REVERT: I 32 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7846 (mtt-85) REVERT: b2 33 LEU cc_start: 0.8225 (tm) cc_final: 0.7916 (tm) REVERT: b1 40 ARG cc_start: 0.5785 (ttt90) cc_final: 0.5365 (ptp-170) REVERT: c9 58 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6417 (mm) outliers start: 14 outliers final: 4 residues processed: 793 average time/residue: 1.5050 time to fit residues: 1420.1234 Evaluate side-chains 511 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 506 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain c9 residue 58 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 8.9990 chunk 353 optimal weight: 50.0000 chunk 196 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 238 optimal weight: 0.0010 chunk 189 optimal weight: 2.9990 chunk 366 optimal weight: 30.0000 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: 0.6788 ------------------------------------------------------------------------------- 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 57 ASN B 147 GLN B 186 GLN B 322 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS C 18 ASN C 186 GLN 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 119 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** c5 23 ASN c7 23 ASN c7 37 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35578 Z= 0.211 Angle : 0.634 10.297 48333 Z= 0.324 Chirality : 0.045 0.221 5788 Planarity : 0.006 0.059 6254 Dihedral : 6.523 82.630 5178 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.92 % Rotamer: Outliers : 3.34 % Allowed : 12.40 % Favored : 84.26 % 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: -0.89 (0.12), residues: 4648 helix: -0.06 (0.10), residues: 2507 sheet: -0.63 (0.22), residues: 544 loop : -1.24 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 206 HIS 0.009 0.001 HIS F 363 PHE 0.020 0.001 PHE A 456 TYR 0.041 0.001 TYRc6 69 ARG 0.007 0.000 ARG A 455 *********************** 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 655 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 538 time to evaluate : 4.137 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 revert: symmetry clash REVERT: A 26 SER cc_start: 0.7604 (m) cc_final: 0.7351 (p) REVERT: A 60 MET cc_start: 0.8695 (mmt) cc_final: 0.8481 (mmm) REVERT: A 182 THR cc_start: 0.8869 (t) cc_final: 0.8664 (m) REVERT: A 214 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8226 (tttp) REVERT: A 250 MET cc_start: 0.8888 (ttp) cc_final: 0.8531 (ttp) REVERT: A 347 ASP cc_start: 0.7433 (m-30) cc_final: 0.7224 (m-30) REVERT: A 373 LYS cc_start: 0.8144 (ttmt) cc_final: 0.7925 (ttpp) REVERT: A 385 ASP cc_start: 0.7793 (m-30) cc_final: 0.7560 (m-30) REVERT: A 458 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7705 (tttm) REVERT: A 463 PHE cc_start: 0.7470 (t80) cc_final: 0.7091 (t80) REVERT: A 492 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7636 (mm-30) REVERT: B 62 MET cc_start: 0.7989 (ttp) cc_final: 0.7785 (ttm) REVERT: B 214 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8260 (mtmt) REVERT: B 273 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8410 (tp) REVERT: B 306 ASP cc_start: 0.8007 (m-30) cc_final: 0.7778 (m-30) REVERT: B 473 GLU cc_start: 0.7440 (tp30) cc_final: 0.7184 (mm-30) REVERT: C 62 MET cc_start: 0.8338 (ttt) cc_final: 0.8040 (ttm) REVERT: C 250 MET cc_start: 0.9084 (ttp) cc_final: 0.8738 (ttm) REVERT: C 262 ASP cc_start: 0.7495 (m-30) cc_final: 0.7157 (m-30) REVERT: C 467 ASN cc_start: 0.7334 (m-40) cc_final: 0.6924 (m110) REVERT: C 469 GLN cc_start: 0.6466 (tm-30) cc_final: 0.6239 (tm-30) REVERT: D 75 GLU cc_start: 0.7666 (tt0) cc_final: 0.7216 (tm-30) REVERT: D 332 GLU cc_start: 0.7633 (tp30) cc_final: 0.7331 (tp30) REVERT: D 381 GLN cc_start: 0.7920 (tt0) cc_final: 0.6908 (tp40) REVERT: D 431 LYS cc_start: 0.7734 (mtpm) cc_final: 0.7483 (mtpt) REVERT: D 467 LYS cc_start: 0.7590 (mtmt) cc_final: 0.6894 (mptt) REVERT: E 17 LYS cc_start: 0.8384 (tttm) cc_final: 0.8175 (tttt) REVERT: E 39 GLU cc_start: 0.7905 (pm20) cc_final: 0.7695 (pm20) REVERT: E 90 VAL cc_start: 0.8674 (m) cc_final: 0.8439 (p) REVERT: E 135 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8203 (tp) REVERT: E 167 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8275 (tp) REVERT: E 243 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: E 329 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8624 (p) REVERT: E 332 GLU cc_start: 0.7035 (tp30) cc_final: 0.6753 (tp30) REVERT: E 375 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7674 (mm-40) REVERT: E 419 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: F 89 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: F 419 GLN cc_start: 0.7793 (pt0) cc_final: 0.7590 (pt0) REVERT: F 438 LYS cc_start: 0.7941 (tttt) cc_final: 0.7640 (ttpp) REVERT: F 469 MET cc_start: 0.7913 (mtp) cc_final: 0.7505 (mtm) REVERT: G 8 LYS cc_start: 0.8217 (tptt) cc_final: 0.7998 (tptt) REVERT: G 40 LYS cc_start: 0.7889 (mtpm) cc_final: 0.7517 (ttpp) REVERT: b2 33 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7720 (tm) REVERT: a 157 ILE cc_start: 0.8922 (pp) cc_final: 0.8603 (pp) REVERT: a 171 PHE cc_start: 0.6821 (t80) cc_final: 0.6516 (t80) REVERT: c6 48 MET cc_start: 0.6753 (ttm) cc_final: 0.6472 (ttt) REVERT: c7 30 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7945 (t) REVERT: c9 58 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6447 (mm) outliers start: 117 outliers final: 40 residues processed: 616 average time/residue: 1.3538 time to fit residues: 1015.6345 Evaluate side-chains 519 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 469 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b2 residue 40 ARG Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c5 residue 58 LEU Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c9 residue 58 LEU 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: 0.0980 chunk 352 optimal weight: 50.0000 chunk 288 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 424 optimal weight: 9.9990 chunk 458 optimal weight: 7.9990 chunk 378 optimal weight: 10.0000 chunk 421 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 340 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN C 215 HIS C 466 GLN D 22 HIS D 34 HIS D 119 HIS ** 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 ** 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** c4 37 GLN c7 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35578 Z= 0.199 Angle : 0.607 18.871 48333 Z= 0.302 Chirality : 0.044 0.287 5788 Planarity : 0.005 0.058 6254 Dihedral : 6.143 85.756 5177 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 3.63 % Allowed : 13.54 % Favored : 82.83 % 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: -0.15 (0.12), residues: 4648 helix: 0.59 (0.10), residues: 2497 sheet: -0.40 (0.22), residues: 556 loop : -0.94 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 105 HIS 0.008 0.001 HIS E 363 PHE 0.015 0.001 PHE A 456 TYR 0.030 0.001 TYRc6 69 ARG 0.005 0.000 ARG I 104 *********************** 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 628 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 501 time to evaluate : 3.770 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: A 101 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: A 214 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8247 (tttm) REVERT: A 250 MET cc_start: 0.8886 (ttp) cc_final: 0.8656 (ttp) REVERT: A 373 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7901 (ttpp) REVERT: A 385 ASP cc_start: 0.7783 (m-30) cc_final: 0.7556 (m-30) REVERT: A 458 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7742 (tttp) REVERT: A 463 PHE cc_start: 0.7459 (t80) cc_final: 0.7224 (t80) REVERT: B 161 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8542 (mtt90) REVERT: B 214 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8245 (mtmt) REVERT: B 273 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8505 (tp) REVERT: B 306 ASP cc_start: 0.7993 (m-30) cc_final: 0.7779 (m-30) REVERT: B 465 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: B 473 GLU cc_start: 0.7473 (tp30) cc_final: 0.7188 (mm-30) REVERT: C 250 MET cc_start: 0.9134 (ttp) cc_final: 0.8897 (ttm) REVERT: C 262 ASP cc_start: 0.7513 (m-30) cc_final: 0.7161 (m-30) REVERT: C 383 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7486 (ttp-170) REVERT: C 469 GLN cc_start: 0.6650 (tm-30) cc_final: 0.6353 (tm-30) REVERT: C 484 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7119 (mt-10) REVERT: D 75 GLU cc_start: 0.7702 (tt0) cc_final: 0.7425 (tt0) REVERT: D 332 GLU cc_start: 0.7675 (tp30) cc_final: 0.7382 (tp30) REVERT: D 381 GLN cc_start: 0.7918 (tt0) cc_final: 0.6888 (tp40) REVERT: D 431 LYS cc_start: 0.7757 (mtpm) cc_final: 0.7467 (mtpt) REVERT: E 5 ARG cc_start: 0.7843 (ppt170) cc_final: 0.7496 (ppt170) REVERT: E 17 LYS cc_start: 0.8381 (tttm) cc_final: 0.8114 (tttt) REVERT: E 39 GLU cc_start: 0.7917 (pm20) cc_final: 0.7652 (pm20) REVERT: E 77 ILE cc_start: 0.8908 (pt) cc_final: 0.8480 (mp) REVERT: E 90 VAL cc_start: 0.8762 (m) cc_final: 0.8522 (p) REVERT: E 135 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8313 (tp) REVERT: E 167 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8276 (tp) REVERT: E 237 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7543 (mt-10) REVERT: E 243 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: E 329 THR cc_start: 0.8868 (t) cc_final: 0.8616 (p) REVERT: E 332 GLU cc_start: 0.6945 (tp30) cc_final: 0.6631 (tp30) REVERT: E 381 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6326 (mm110) REVERT: E 419 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: F 89 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: F 365 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: F 438 LYS cc_start: 0.8032 (tttt) cc_final: 0.7655 (ttpp) REVERT: F 455 LEU cc_start: 0.9183 (mt) cc_final: 0.8964 (mt) REVERT: F 460 GLU cc_start: 0.7857 (mp0) cc_final: 0.7446 (mp0) REVERT: F 469 MET cc_start: 0.7860 (mtp) cc_final: 0.7419 (mtm) REVERT: G 8 LYS cc_start: 0.8236 (tptt) cc_final: 0.7841 (tptt) REVERT: G 40 LYS cc_start: 0.7895 (mtpm) cc_final: 0.7495 (ttpp) REVERT: I 83 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7627 (mtt180) REVERT: b2 26 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.6733 (mtm110) REVERT: b2 33 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7828 (tm) REVERT: b1 40 ARG cc_start: 0.5535 (ttt90) cc_final: 0.5096 (ptt180) REVERT: a 171 PHE cc_start: 0.6883 (t80) cc_final: 0.6667 (t80) REVERT: c6 48 MET cc_start: 0.6829 (ttm) cc_final: 0.6442 (ttt) outliers start: 127 outliers final: 51 residues processed: 590 average time/residue: 1.3795 time to fit residues: 986.1916 Evaluate side-chains 528 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 463 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 38 ASN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c6 residue 5 VAL Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c7 residue 50 ILE 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: 8.9990 chunk 220 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 426 optimal weight: 5.9990 chunk 451 optimal weight: 20.0000 chunk 222 optimal weight: 0.9980 chunk 404 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 488 ASN B 215 HIS B 425 HIS B 470 HIS C 422 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN E 401 HIS F 28 ASN F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN I 41 ASN ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35578 Z= 0.351 Angle : 0.658 12.654 48333 Z= 0.330 Chirality : 0.047 0.251 5788 Planarity : 0.005 0.058 6254 Dihedral : 6.261 88.103 5174 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 4.54 % Allowed : 14.31 % Favored : 81.14 % 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: 0.03 (0.12), residues: 4648 helix: 0.76 (0.11), residues: 2501 sheet: -0.60 (0.21), residues: 565 loop : -0.78 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 206 HIS 0.012 0.002 HIS E 363 PHE 0.019 0.002 PHE C 494 TYR 0.027 0.002 TYR E 427 ARG 0.007 0.001 ARG C 90 *********************** 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 647 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 488 time to evaluate : 3.876 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 214 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8254 (tttp) REVERT: A 250 MET cc_start: 0.9012 (ttp) cc_final: 0.8764 (ttp) REVERT: A 262 ASP cc_start: 0.7750 (m-30) cc_final: 0.7377 (m-30) REVERT: A 373 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7960 (ttpp) REVERT: A 455 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7769 (ttm110) REVERT: A 458 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7797 (tttp) REVERT: B 17 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: B 28 VAL cc_start: 0.8846 (t) cc_final: 0.8572 (p) REVERT: B 161 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8606 (mtt90) REVERT: B 214 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8236 (mtmm) REVERT: B 273 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8661 (tp) REVERT: B 306 ASP cc_start: 0.8040 (m-30) cc_final: 0.7821 (m-30) REVERT: B 465 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: B 473 GLU cc_start: 0.7297 (tp30) cc_final: 0.7016 (mm-30) REVERT: C 262 ASP cc_start: 0.7856 (m-30) cc_final: 0.7525 (m-30) REVERT: C 407 GLN cc_start: 0.7866 (mt0) cc_final: 0.7653 (mt0) REVERT: C 469 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6689 (tm-30) REVERT: C 484 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7226 (mt-10) REVERT: D 85 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8217 (p) REVERT: D 218 MET cc_start: 0.9033 (mtt) cc_final: 0.8687 (mtt) REVERT: D 332 GLU cc_start: 0.7749 (tp30) cc_final: 0.7371 (tp30) REVERT: D 381 GLN cc_start: 0.8013 (tt0) cc_final: 0.6946 (tp40) REVERT: D 391 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7451 (mt-10) REVERT: D 431 LYS cc_start: 0.7824 (mtpm) cc_final: 0.7539 (mtpt) REVERT: E 17 LYS cc_start: 0.8507 (tttm) cc_final: 0.8215 (tttt) REVERT: E 39 GLU cc_start: 0.7902 (pm20) cc_final: 0.7629 (pm20) REVERT: E 90 VAL cc_start: 0.8932 (m) cc_final: 0.8696 (p) REVERT: E 329 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8709 (m) REVERT: E 332 GLU cc_start: 0.6938 (tp30) cc_final: 0.6581 (tp30) REVERT: E 381 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6247 (mm110) REVERT: E 419 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: F 89 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: F 365 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.6849 (mp10) REVERT: F 381 GLN cc_start: 0.8411 (tp40) cc_final: 0.8131 (mm-40) REVERT: F 438 LYS cc_start: 0.8167 (tttt) cc_final: 0.7751 (ttpp) REVERT: F 460 GLU cc_start: 0.8086 (mp0) cc_final: 0.7786 (mp0) REVERT: F 467 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7801 (ptpp) REVERT: F 469 MET cc_start: 0.7825 (mtp) cc_final: 0.7461 (mtm) REVERT: G 4 LEU cc_start: 0.8529 (tp) cc_final: 0.8270 (tp) REVERT: G 40 LYS cc_start: 0.8013 (mtpm) cc_final: 0.7525 (ttpp) REVERT: G 100 TYR cc_start: 0.7947 (t80) cc_final: 0.7552 (t80) REVERT: G 231 ASP cc_start: 0.8405 (t70) cc_final: 0.8186 (t0) REVERT: I 155 ARG cc_start: 0.7620 (ttt90) cc_final: 0.7197 (tpt-90) REVERT: b2 33 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7786 (tm) REVERT: b1 27 LYS cc_start: 0.8690 (tptt) cc_final: 0.8465 (tptp) REVERT: c6 6 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6410 (tt) REVERT: c6 48 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6636 (ttt) REVERT: c7 30 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.8002 (t) outliers start: 159 outliers final: 74 residues processed: 602 average time/residue: 1.4170 time to fit residues: 1034.2650 Evaluate side-chains 550 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 459 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 12 ILE Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c6 residue 6 LEU Chi-restraints excluded: chain c6 residue 48 MET Chi-restraints excluded: chain c7 residue 10 ILE Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c7 residue 50 ILE 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: 0.0970 chunk 6 optimal weight: 3.9990 chunk 336 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 385 optimal weight: 10.0000 chunk 312 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 405 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS F 28 ASN F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 207 GLN ** a 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35578 Z= 0.260 Angle : 0.620 16.558 48333 Z= 0.308 Chirality : 0.045 0.309 5788 Planarity : 0.004 0.059 6254 Dihedral : 6.074 83.235 5174 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 4.09 % Allowed : 15.43 % Favored : 80.49 % 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: 0.29 (0.12), residues: 4648 helix: 0.95 (0.11), residues: 2501 sheet: -0.52 (0.21), residues: 561 loop : -0.62 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP a 206 HIS 0.008 0.001 HIS E 363 PHE 0.013 0.001 PHE B 463 TYR 0.023 0.001 TYR B 438 ARG 0.006 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 621 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 478 time to evaluate : 3.753 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: A 214 LYS cc_start: 0.8459 (mtmt) cc_final: 0.8252 (tttp) REVERT: A 250 MET cc_start: 0.8980 (ttp) cc_final: 0.8737 (ttp) REVERT: A 262 ASP cc_start: 0.7619 (m-30) cc_final: 0.7231 (m-30) REVERT: A 373 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7932 (ttpp) REVERT: A 455 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7733 (ttm110) REVERT: A 458 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7813 (tttp) REVERT: B 17 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: B 28 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 161 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8582 (mtt90) REVERT: B 214 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8225 (mtmm) REVERT: B 273 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8597 (tp) REVERT: B 306 ASP cc_start: 0.8034 (m-30) cc_final: 0.7816 (m-30) REVERT: B 465 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: B 473 GLU cc_start: 0.7286 (tp30) cc_final: 0.6976 (mm-30) REVERT: C 262 ASP cc_start: 0.7717 (m-30) cc_final: 0.7376 (m-30) REVERT: C 383 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7739 (ttp-110) REVERT: C 469 GLN cc_start: 0.6993 (tm-30) cc_final: 0.6568 (tm-30) REVERT: C 484 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7169 (mt-10) REVERT: D 85 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8284 (p) REVERT: D 332 GLU cc_start: 0.7748 (tp30) cc_final: 0.7358 (tp30) REVERT: D 381 GLN cc_start: 0.7927 (tt0) cc_final: 0.6887 (tp40) REVERT: D 391 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 431 LYS cc_start: 0.7795 (mtpm) cc_final: 0.7564 (mtpt) REVERT: E 17 LYS cc_start: 0.8525 (tttm) cc_final: 0.8183 (tttt) REVERT: E 39 GLU cc_start: 0.7849 (pm20) cc_final: 0.7563 (pm20) REVERT: E 77 ILE cc_start: 0.9021 (pt) cc_final: 0.8646 (mp) REVERT: E 90 VAL cc_start: 0.8936 (m) cc_final: 0.8720 (p) REVERT: E 167 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8300 (tp) REVERT: E 332 GLU cc_start: 0.6984 (tp30) cc_final: 0.6612 (tp30) REVERT: E 381 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.6291 (mm110) REVERT: E 419 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: E 454 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7263 (ttm-80) REVERT: F 365 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6787 (mp10) REVERT: F 381 GLN cc_start: 0.8307 (tp40) cc_final: 0.8016 (mm-40) REVERT: F 438 LYS cc_start: 0.8223 (tttt) cc_final: 0.7828 (ttpp) REVERT: F 455 LEU cc_start: 0.9190 (mt) cc_final: 0.8953 (mt) REVERT: F 460 GLU cc_start: 0.8064 (mp0) cc_final: 0.7699 (mp0) REVERT: F 467 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7862 (ptpp) REVERT: F 469 MET cc_start: 0.7786 (mtp) cc_final: 0.7488 (mtm) REVERT: G 4 LEU cc_start: 0.8483 (tp) cc_final: 0.8240 (tp) REVERT: G 6 ASP cc_start: 0.7362 (m-30) cc_final: 0.6920 (m-30) REVERT: G 40 LYS cc_start: 0.8016 (mtpm) cc_final: 0.7515 (ttpp) REVERT: G 98 LEU cc_start: 0.8071 (tp) cc_final: 0.7846 (tp) REVERT: I 64 GLU cc_start: 0.8064 (tt0) cc_final: 0.7299 (mp0) REVERT: I 155 ARG cc_start: 0.7612 (ttt90) cc_final: 0.7220 (tpt-90) REVERT: b2 33 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7775 (tm) REVERT: b1 40 ARG cc_start: 0.5258 (ttt90) cc_final: 0.4817 (ptt180) REVERT: a 171 PHE cc_start: 0.6862 (t80) cc_final: 0.6628 (t80) REVERT: c6 48 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6547 (ttt) REVERT: c7 30 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.8016 (t) REVERT: c7 50 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6993 (pt) outliers start: 143 outliers final: 64 residues processed: 582 average time/residue: 1.4247 time to fit residues: 1013.0515 Evaluate side-chains 530 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 449 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 467 LYS Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 25 LEU Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c6 residue 48 MET Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c7 residue 50 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 0.7980 chunk 406 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 265 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 451 optimal weight: 0.9990 chunk 375 optimal weight: 0.2980 chunk 209 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN C 397 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** ** F 330 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35578 Z= 0.180 Angle : 0.579 16.038 48333 Z= 0.287 Chirality : 0.043 0.267 5788 Planarity : 0.004 0.061 6254 Dihedral : 5.826 77.218 5174 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 3.29 % Allowed : 17.46 % Favored : 79.26 % 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: 0.58 (0.13), residues: 4648 helix: 1.16 (0.11), residues: 2500 sheet: -0.38 (0.22), residues: 571 loop : -0.44 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 206 HIS 0.006 0.001 HIS E 363 PHE 0.027 0.001 PHE a 87 TYR 0.019 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 610 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 495 time to evaluate : 3.829 Fit side-chains revert: symmetry clash 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 REVERT: A 171 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8198 (ttp-110) REVERT: A 250 MET cc_start: 0.8927 (ttp) cc_final: 0.8654 (ttp) REVERT: A 373 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7878 (ttpp) REVERT: A 455 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7717 (ttm110) REVERT: A 458 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7821 (tttp) REVERT: B 17 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: B 122 GLU cc_start: 0.6817 (pm20) cc_final: 0.6473 (mp0) REVERT: B 214 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8140 (mtmt) REVERT: B 306 ASP cc_start: 0.8035 (m-30) cc_final: 0.7806 (m-30) REVERT: B 465 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: B 473 GLU cc_start: 0.7269 (tp30) cc_final: 0.6968 (mm-30) REVERT: C 383 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7714 (ttp-170) REVERT: C 469 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6487 (tm-30) REVERT: C 484 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7112 (mt-10) REVERT: D 85 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8284 (p) REVERT: D 332 GLU cc_start: 0.7738 (tp30) cc_final: 0.7362 (tp30) REVERT: D 381 GLN cc_start: 0.7911 (tt0) cc_final: 0.6879 (tp40) REVERT: D 391 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7334 (mt-10) REVERT: D 431 LYS cc_start: 0.7820 (mtpm) cc_final: 0.7535 (mtpt) REVERT: D 432 GLU cc_start: 0.7780 (mp0) cc_final: 0.7512 (mp0) REVERT: E 5 ARG cc_start: 0.7738 (ppt170) cc_final: 0.7349 (ptp-110) REVERT: E 17 LYS cc_start: 0.8491 (tttm) cc_final: 0.8137 (tttt) REVERT: E 77 ILE cc_start: 0.9063 (pt) cc_final: 0.8606 (mp) REVERT: E 90 VAL cc_start: 0.8905 (m) cc_final: 0.8697 (p) REVERT: E 167 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8276 (tp) REVERT: E 332 GLU cc_start: 0.6972 (tp30) cc_final: 0.6622 (tp30) REVERT: E 381 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6254 (mm110) REVERT: E 419 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: F 118 ILE cc_start: 0.8869 (mt) cc_final: 0.8583 (mm) REVERT: F 381 GLN cc_start: 0.8327 (tp40) cc_final: 0.8071 (mm-40) REVERT: F 438 LYS cc_start: 0.8225 (tttt) cc_final: 0.7796 (ttpp) REVERT: F 455 LEU cc_start: 0.9177 (mt) cc_final: 0.8939 (mt) REVERT: F 460 GLU cc_start: 0.8061 (mp0) cc_final: 0.7723 (mp0) REVERT: F 469 MET cc_start: 0.7805 (mtp) cc_final: 0.7432 (mtm) REVERT: G 6 ASP cc_start: 0.7375 (m-30) cc_final: 0.6976 (m-30) REVERT: G 40 LYS cc_start: 0.7936 (mtpm) cc_final: 0.7484 (ttpp) REVERT: G 98 LEU cc_start: 0.8072 (tp) cc_final: 0.7839 (tp) REVERT: I 131 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8442 (pm20) REVERT: I 155 ARG cc_start: 0.7581 (ttt90) cc_final: 0.7224 (tpt-90) REVERT: b2 17 MET cc_start: 0.4258 (ppp) cc_final: 0.3764 (ppp) REVERT: b2 33 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7478 (tm) REVERT: b1 40 ARG cc_start: 0.5233 (ttt90) cc_final: 0.4848 (ptt180) REVERT: a 157 ILE cc_start: 0.8854 (pp) cc_final: 0.8493 (pp) REVERT: a 160 PHE cc_start: 0.7990 (m-80) cc_final: 0.7776 (m-80) REVERT: c6 48 MET cc_start: 0.6923 (ttm) cc_final: 0.6559 (ttt) REVERT: c7 30 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7946 (t) REVERT: c7 50 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6886 (pt) REVERT: c8 50 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5427 (tp) outliers start: 115 outliers final: 59 residues processed: 581 average time/residue: 1.4471 time to fit residues: 1016.4292 Evaluate side-chains 539 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 467 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 455 ARG Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 24 LEU Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 63 ILE Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 50 ILE Chi-restraints excluded: chain c9 residue 6 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 329 optimal weight: 0.2980 chunk 255 optimal weight: 0.6980 chunk 380 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 450 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 274 optimal weight: 0.5980 chunk 207 optimal weight: 0.0570 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 433 GLN B 172 GLN C 397 GLN E 304 GLN E 401 HIS F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35578 Z= 0.174 Angle : 0.580 15.419 48333 Z= 0.286 Chirality : 0.043 0.290 5788 Planarity : 0.004 0.061 6254 Dihedral : 5.714 74.481 5174 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 3.43 % Allowed : 17.83 % Favored : 78.74 % 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: 0.76 (0.13), residues: 4648 helix: 1.29 (0.11), residues: 2498 sheet: -0.27 (0.22), residues: 567 loop : -0.34 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 206 HIS 0.005 0.001 HIS E 363 PHE 0.024 0.001 PHE A 456 TYR 0.021 0.001 TYR B 438 ARG 0.016 0.000 ARGb2 26 *********************** REFINEMENT MACRO_CYCLE 7 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 603 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 483 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash 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: A 166 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 171 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8168 (ttp-110) REVERT: A 250 MET cc_start: 0.8873 (ttp) cc_final: 0.8621 (ttp) REVERT: A 373 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7864 (ttpp) REVERT: A 458 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7749 (tttp) REVERT: B 17 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: B 122 GLU cc_start: 0.6937 (pm20) cc_final: 0.6612 (mp0) REVERT: B 161 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8589 (mtt90) REVERT: B 214 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8231 (mtmt) REVERT: B 273 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8560 (tp) REVERT: B 306 ASP cc_start: 0.8027 (m-30) cc_final: 0.7798 (m-30) REVERT: B 465 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: B 473 GLU cc_start: 0.7241 (tp30) cc_final: 0.6939 (mm-30) REVERT: C 383 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7778 (ttp-110) REVERT: C 469 GLN cc_start: 0.6781 (tm-30) cc_final: 0.6405 (tm-30) REVERT: C 484 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7016 (mt-10) REVERT: D 85 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8287 (p) REVERT: D 254 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7823 (pp) REVERT: D 332 GLU cc_start: 0.7721 (tp30) cc_final: 0.7346 (tp30) REVERT: D 381 GLN cc_start: 0.7823 (tt0) cc_final: 0.6834 (tp40) REVERT: D 431 LYS cc_start: 0.7777 (mtpm) cc_final: 0.7534 (mtpt) REVERT: E 5 ARG cc_start: 0.7711 (ppt170) cc_final: 0.7360 (ptp-110) REVERT: E 77 ILE cc_start: 0.9069 (pt) cc_final: 0.8592 (mp) REVERT: E 90 VAL cc_start: 0.8888 (m) cc_final: 0.8684 (p) REVERT: E 167 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8334 (tp) REVERT: E 243 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: E 332 GLU cc_start: 0.6998 (tp30) cc_final: 0.6605 (tp30) REVERT: E 381 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.6202 (mm110) REVERT: E 407 GLN cc_start: 0.7951 (tt0) cc_final: 0.7702 (tt0) REVERT: E 419 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: F 108 ASP cc_start: 0.7595 (t0) cc_final: 0.7384 (m-30) REVERT: F 118 ILE cc_start: 0.8801 (mt) cc_final: 0.8541 (mm) REVERT: F 168 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8409 (tt) REVERT: F 381 GLN cc_start: 0.8163 (tp40) cc_final: 0.7902 (mm-40) REVERT: F 438 LYS cc_start: 0.8180 (tttt) cc_final: 0.7721 (ttpp) REVERT: F 455 LEU cc_start: 0.9233 (mt) cc_final: 0.8926 (mt) REVERT: F 460 GLU cc_start: 0.8037 (mp0) cc_final: 0.7726 (mp0) REVERT: F 469 MET cc_start: 0.7809 (mtp) cc_final: 0.7547 (mtp) REVERT: G 6 ASP cc_start: 0.7352 (m-30) cc_final: 0.6972 (m-30) REVERT: G 40 LYS cc_start: 0.7894 (mtpm) cc_final: 0.7474 (ttpp) REVERT: G 98 LEU cc_start: 0.8046 (tp) cc_final: 0.7806 (tp) REVERT: I 131 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8426 (pm20) REVERT: I 155 ARG cc_start: 0.7550 (ttt90) cc_final: 0.7230 (tpt-90) REVERT: b2 25 LEU cc_start: 0.5008 (mm) cc_final: 0.2808 (mm) REVERT: b2 31 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.7030 (mp10) REVERT: b2 33 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7633 (tm) REVERT: b1 40 ARG cc_start: 0.5145 (ttt90) cc_final: 0.4787 (ptt180) REVERT: a 119 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7218 (mp) REVERT: a 160 PHE cc_start: 0.7921 (m-80) cc_final: 0.7694 (m-80) REVERT: c6 48 MET cc_start: 0.6844 (ttm) cc_final: 0.6490 (ttt) REVERT: c7 30 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7952 (t) outliers start: 120 outliers final: 59 residues processed: 576 average time/residue: 1.3983 time to fit residues: 974.5773 Evaluate side-chains 533 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 456 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 31 GLN Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c7 residue 30 THR Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c9 residue 6 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 286 optimal weight: 0.5980 chunk 306 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 353 optimal weight: 100.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN C 397 GLN D 22 HIS E 401 HIS F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN I 95 GLN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35578 Z= 0.303 Angle : 0.644 20.819 48333 Z= 0.316 Chirality : 0.046 0.369 5788 Planarity : 0.005 0.090 6254 Dihedral : 5.945 82.269 5174 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 3.31 % Allowed : 18.17 % Favored : 78.51 % 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: 0.64 (0.13), residues: 4648 helix: 1.18 (0.11), residues: 2503 sheet: -0.36 (0.22), residues: 560 loop : -0.36 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 206 HIS 0.008 0.001 HIS F 363 PHE 0.036 0.002 PHE a 96 TYR 0.021 0.001 TYR B 438 ARG 0.018 0.001 ARGb2 26 *********************** REFINEMENT MACRO_CYCLE 8 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 576 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 460 time to evaluate : 3.886 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: A 262 ASP cc_start: 0.7649 (m-30) cc_final: 0.7288 (m-30) REVERT: A 373 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7947 (ttpp) REVERT: A 458 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7757 (tttp) REVERT: B 17 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 122 GLU cc_start: 0.6897 (pm20) cc_final: 0.6586 (mp0) REVERT: B 161 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8628 (mtt90) REVERT: B 214 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8252 (mtmm) REVERT: B 273 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (tp) REVERT: B 306 ASP cc_start: 0.8051 (m-30) cc_final: 0.7823 (m-30) REVERT: B 465 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7425 (m-30) REVERT: B 473 GLU cc_start: 0.7305 (tp30) cc_final: 0.6975 (mm-30) REVERT: C 89 ARG cc_start: 0.7218 (ttp-110) cc_final: 0.6833 (ttp80) REVERT: C 262 ASP cc_start: 0.7779 (m-30) cc_final: 0.7469 (m-30) REVERT: C 383 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7752 (ttp-110) REVERT: C 469 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6640 (tm-30) REVERT: C 484 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7097 (mt-10) REVERT: D 85 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8315 (p) REVERT: D 254 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8074 (pp) REVERT: D 332 GLU cc_start: 0.7794 (tp30) cc_final: 0.7396 (tp30) REVERT: D 381 GLN cc_start: 0.7906 (tt0) cc_final: 0.6887 (tp40) REVERT: D 431 LYS cc_start: 0.7823 (mtpm) cc_final: 0.7571 (mtpt) REVERT: E 5 ARG cc_start: 0.7781 (ppt170) cc_final: 0.7368 (ptp-110) REVERT: E 332 GLU cc_start: 0.7038 (tp30) cc_final: 0.6619 (tp30) REVERT: E 381 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.6104 (mm110) REVERT: E 419 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: F 118 ILE cc_start: 0.8963 (mt) cc_final: 0.8671 (mm) REVERT: F 168 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8539 (tt) REVERT: F 365 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: F 381 GLN cc_start: 0.8205 (tp40) cc_final: 0.7942 (mm-40) REVERT: F 438 LYS cc_start: 0.8247 (tttt) cc_final: 0.7813 (ttpp) REVERT: F 455 LEU cc_start: 0.9189 (mt) cc_final: 0.8950 (mt) REVERT: F 460 GLU cc_start: 0.8159 (mp0) cc_final: 0.7825 (mp0) REVERT: F 469 MET cc_start: 0.7809 (mtp) cc_final: 0.7488 (mtm) REVERT: G 4 LEU cc_start: 0.8488 (tp) cc_final: 0.8209 (tp) REVERT: G 6 ASP cc_start: 0.7365 (m-30) cc_final: 0.6929 (m-30) REVERT: G 40 LYS cc_start: 0.8000 (mtpm) cc_final: 0.7526 (ttpp) REVERT: G 98 LEU cc_start: 0.8094 (tp) cc_final: 0.7834 (tp) REVERT: I 131 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8425 (pm20) REVERT: I 155 ARG cc_start: 0.7659 (ttt90) cc_final: 0.7246 (tpt-90) REVERT: b2 31 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: b2 33 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7743 (tm) REVERT: a 160 PHE cc_start: 0.7910 (m-80) cc_final: 0.7651 (m-80) REVERT: a 203 MET cc_start: 0.5262 (mmm) cc_final: 0.4840 (mmm) REVERT: c6 48 MET cc_start: 0.6791 (ttm) cc_final: 0.6464 (ttt) REVERT: c8 50 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5077 (tp) outliers start: 116 outliers final: 71 residues processed: 545 average time/residue: 1.4124 time to fit residues: 939.8631 Evaluate side-chains 535 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 450 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 31 GLN Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain b1 residue 25 LEU Chi-restraints excluded: chain b1 residue 39 GLN Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 207 GLN Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c7 residue 43 VAL Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 50 ILE Chi-restraints excluded: chain c9 residue 6 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 6.9990 chunk 431 optimal weight: 6.9990 chunk 393 optimal weight: 40.0000 chunk 419 optimal weight: 20.0000 chunk 252 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 379 optimal weight: 7.9990 chunk 396 optimal weight: 5.9990 chunk 417 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN D 22 HIS E 401 HIS F 177 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 35578 Z= 0.461 Angle : 0.714 18.803 48333 Z= 0.352 Chirality : 0.049 0.283 5788 Planarity : 0.005 0.104 6254 Dihedral : 6.308 86.830 5174 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer: Outliers : 3.31 % Allowed : 18.31 % Favored : 78.37 % 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: 0.37 (0.12), residues: 4648 helix: 0.98 (0.11), residues: 2507 sheet: -0.49 (0.21), residues: 578 loop : -0.51 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 54 HIS 0.011 0.002 HIS F 363 PHE 0.034 0.002 PHE a 96 TYR 0.021 0.002 TYR B 438 ARG 0.022 0.001 ARGb2 26 *********************** REFINEMENT MACRO_CYCLE 9 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 567 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 451 time to evaluate : 3.740 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: A 26 SER cc_start: 0.7549 (m) cc_final: 0.7248 (p) REVERT: A 262 ASP cc_start: 0.7905 (m-30) cc_final: 0.7527 (m-30) REVERT: A 373 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7994 (ttpp) REVERT: A 458 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7818 (tttp) REVERT: B 17 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: B 122 GLU cc_start: 0.6797 (pm20) cc_final: 0.6500 (mp0) REVERT: B 214 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8279 (mtmt) REVERT: B 273 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8672 (tp) REVERT: B 306 ASP cc_start: 0.8035 (m-30) cc_final: 0.7826 (m-30) REVERT: B 457 GLU cc_start: 0.8072 (pt0) cc_final: 0.7802 (pt0) REVERT: B 465 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: B 473 GLU cc_start: 0.7457 (tp30) cc_final: 0.7073 (mm-30) REVERT: C 62 MET cc_start: 0.8430 (ttt) cc_final: 0.8159 (ttm) REVERT: C 89 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.6863 (ttp80) REVERT: C 262 ASP cc_start: 0.8009 (m-30) cc_final: 0.7677 (m-30) REVERT: C 383 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7808 (ttp-110) REVERT: C 407 GLN cc_start: 0.7830 (mt0) cc_final: 0.7607 (tp40) REVERT: C 466 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: C 484 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7262 (mt-10) REVERT: D 85 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8265 (p) REVERT: D 254 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8104 (pp) REVERT: D 332 GLU cc_start: 0.7760 (tp30) cc_final: 0.7358 (tp30) REVERT: D 381 GLN cc_start: 0.7959 (tt0) cc_final: 0.6935 (tp40) REVERT: D 431 LYS cc_start: 0.7831 (mtpm) cc_final: 0.7568 (mtpt) REVERT: E 5 ARG cc_start: 0.7892 (ppt170) cc_final: 0.7411 (ptp-110) REVERT: E 332 GLU cc_start: 0.7129 (tp30) cc_final: 0.6710 (tp30) REVERT: E 381 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6164 (mm110) REVERT: E 419 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: E 435 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7335 (ttp80) REVERT: F 44 ILE cc_start: 0.8578 (mt) cc_final: 0.8356 (mm) REVERT: F 118 ILE cc_start: 0.9029 (mt) cc_final: 0.8723 (mm) REVERT: F 168 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8656 (tt) REVERT: F 249 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8531 (tt) REVERT: F 365 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.6583 (mp10) REVERT: F 381 GLN cc_start: 0.8253 (tp40) cc_final: 0.7965 (mm-40) REVERT: F 438 LYS cc_start: 0.8270 (tttt) cc_final: 0.7815 (ttpp) REVERT: F 469 MET cc_start: 0.7825 (mtp) cc_final: 0.7509 (mtm) REVERT: G 4 LEU cc_start: 0.8568 (tp) cc_final: 0.8291 (tp) REVERT: G 40 LYS cc_start: 0.7997 (mtpm) cc_final: 0.7413 (ttpp) REVERT: G 98 LEU cc_start: 0.8109 (tp) cc_final: 0.7848 (tp) REVERT: G 100 TYR cc_start: 0.8022 (t80) cc_final: 0.7624 (t80) REVERT: I 131 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8445 (pm20) REVERT: I 155 ARG cc_start: 0.7699 (ttt90) cc_final: 0.7183 (tpt-90) REVERT: b2 17 MET cc_start: 0.4715 (ppp) cc_final: 0.3777 (ppp) REVERT: b2 33 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7932 (tm) REVERT: a 119 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7144 (mp) REVERT: a 157 ILE cc_start: 0.8856 (pp) cc_final: 0.8476 (pp) REVERT: a 160 PHE cc_start: 0.7922 (m-80) cc_final: 0.7654 (m-80) REVERT: c6 48 MET cc_start: 0.6915 (ttm) cc_final: 0.6649 (ttt) REVERT: c8 50 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5320 (tp) outliers start: 116 outliers final: 74 residues processed: 539 average time/residue: 1.3971 time to fit residues: 912.0782 Evaluate side-chains 532 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 443 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain a residue 207 GLN Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 50 ILE Chi-restraints excluded: chain c9 residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 0.7980 chunk 443 optimal weight: 4.9990 chunk 270 optimal weight: 0.0010 chunk 210 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 465 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 chunk 370 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 286 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 425 HIS B 172 GLN D 22 HIS E 401 HIS F 177 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3320 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= 0.200 Angle : 0.611 16.331 48333 Z= 0.301 Chirality : 0.044 0.291 5788 Planarity : 0.005 0.156 6254 Dihedral : 5.930 79.416 5174 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 2.60 % Allowed : 19.23 % Favored : 78.17 % 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: 0.64 (0.13), residues: 4648 helix: 1.22 (0.11), residues: 2477 sheet: -0.34 (0.22), residues: 548 loop : -0.42 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPb2 30 HIS 0.007 0.001 HIS C 42 PHE 0.033 0.001 PHE a 96 TYR 0.022 0.001 TYR B 438 ARG 0.010 0.000 ARGb2 40 ********************** REFINEMENT MACRO_CYCLE 10 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 552 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 461 time to evaluate : 3.919 Fit side-chains revert: symmetry clash 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: A 373 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7931 (ttpp) REVERT: A 402 LEU cc_start: 0.6961 (mp) cc_final: 0.6627 (tt) REVERT: B 17 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: B 83 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8157 (mtpt) REVERT: B 122 GLU cc_start: 0.6780 (pm20) cc_final: 0.6426 (mp0) REVERT: B 214 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8249 (mtmm) REVERT: B 273 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8583 (tp) REVERT: B 306 ASP cc_start: 0.8034 (m-30) cc_final: 0.7796 (m-30) REVERT: B 465 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: B 473 GLU cc_start: 0.7348 (tp30) cc_final: 0.6976 (mm-30) REVERT: C 62 MET cc_start: 0.8243 (ttt) cc_final: 0.7978 (ttm) REVERT: C 113 GLN cc_start: 0.8137 (mp10) cc_final: 0.7680 (mt0) REVERT: C 250 MET cc_start: 0.9081 (ttp) cc_final: 0.8866 (ttm) REVERT: C 383 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7717 (ttp-110) REVERT: C 469 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6700 (tm-30) REVERT: C 484 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7038 (mt-10) REVERT: D 35 LYS cc_start: 0.7758 (mmmm) cc_final: 0.7504 (mmmt) REVERT: D 85 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8281 (p) REVERT: D 254 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7964 (pp) REVERT: D 332 GLU cc_start: 0.7712 (tp30) cc_final: 0.7340 (tp30) REVERT: D 381 GLN cc_start: 0.7884 (tt0) cc_final: 0.6861 (tp40) REVERT: D 431 LYS cc_start: 0.7827 (mtpm) cc_final: 0.7587 (mtpt) REVERT: E 5 ARG cc_start: 0.7835 (ppt170) cc_final: 0.7557 (ppt170) REVERT: E 167 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8305 (tp) REVERT: E 332 GLU cc_start: 0.7048 (tp30) cc_final: 0.6633 (tp30) REVERT: E 381 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6229 (mm110) REVERT: E 419 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: F 44 ILE cc_start: 0.8503 (mt) cc_final: 0.8277 (mm) REVERT: F 118 ILE cc_start: 0.8866 (mt) cc_final: 0.8590 (mm) REVERT: F 168 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8433 (tt) REVERT: F 249 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8501 (tt) REVERT: F 365 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6547 (mp10) REVERT: F 381 GLN cc_start: 0.8157 (tp40) cc_final: 0.7888 (mm-40) REVERT: F 438 LYS cc_start: 0.8262 (tttt) cc_final: 0.7807 (ttpp) REVERT: F 455 LEU cc_start: 0.9123 (mt) cc_final: 0.8880 (mt) REVERT: F 460 GLU cc_start: 0.8148 (mp0) cc_final: 0.7816 (mp0) REVERT: F 469 MET cc_start: 0.7780 (mtp) cc_final: 0.7453 (mtm) REVERT: G 6 ASP cc_start: 0.7308 (m-30) cc_final: 0.6893 (m-30) REVERT: G 40 LYS cc_start: 0.8027 (mtpm) cc_final: 0.7524 (ttpp) REVERT: G 98 LEU cc_start: 0.8111 (tp) cc_final: 0.7867 (tp) REVERT: I 131 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8433 (pm20) REVERT: I 155 ARG cc_start: 0.7688 (ttt90) cc_final: 0.7235 (tpt-90) REVERT: I 169 LEU cc_start: 0.7730 (mm) cc_final: 0.7466 (mm) REVERT: b2 17 MET cc_start: 0.4753 (ppp) cc_final: 0.3771 (ppp) REVERT: b2 33 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8067 (tm) REVERT: a 119 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7189 (mp) REVERT: a 157 ILE cc_start: 0.8843 (pp) cc_final: 0.8465 (pp) REVERT: a 160 PHE cc_start: 0.7911 (m-80) cc_final: 0.7638 (m-80) REVERT: c6 48 MET cc_start: 0.6899 (ttm) cc_final: 0.6480 (ttt) REVERT: c8 50 ILE cc_start: 0.5769 (OUTLIER) cc_final: 0.5166 (tp) outliers start: 91 outliers final: 60 residues processed: 534 average time/residue: 1.4522 time to fit residues: 937.0481 Evaluate side-chains 519 residues out of total 3799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 444 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 465 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 383 ARG Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 207 VAL Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain b2 residue 33 LEU Chi-restraints excluded: chain b2 residue 36 ILE Chi-restraints excluded: chain b1 residue 12 ILE Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 92 LEU Chi-restraints excluded: chain a residue 119 LEU Chi-restraints excluded: chain a residue 207 GLN Chi-restraints excluded: chain c0 residue 30 THR Chi-restraints excluded: chain c0 residue 60 ILE Chi-restraints excluded: chain c0 residue 68 ILE Chi-restraints excluded: chain c3 residue 64 VAL Chi-restraints excluded: chain c7 residue 50 ILE Chi-restraints excluded: chain c8 residue 50 ILE Chi-restraints excluded: chain c9 residue 6 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 2.9990 chunk 394 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 341 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 371 optimal weight: 50.0000 chunk 155 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 426 GLN B 172 GLN C 397 GLN D 22 HIS E 401 HIS F 177 GLN I 95 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.180491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121422 restraints weight = 36915.138| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.59 r_work: 0.2851 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35578 Z= 0.329 Angle : 0.669 17.673 48333 Z= 0.329 Chirality : 0.047 0.241 5788 Planarity : 0.005 0.110 6254 Dihedral : 6.101 87.012 5174 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 2.80 % Allowed : 19.34 % Favored : 77.86 % 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: 0.52 (0.12), residues: 4648 helix: 1.12 (0.11), residues: 2490 sheet: -0.38 (0.22), residues: 553 loop : -0.49 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPb2 30 HIS 0.009 0.001 HIS E 363 PHE 0.032 0.002 PHE a 96 TYR 0.021 0.002 TYR B 438 ARG 0.007 0.001 ARG G 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14652.62 seconds wall clock time: 258 minutes 7.76 seconds (15487.76 seconds total)