Starting phenix.real_space_refine on Sat Sep 28 19:37:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/09_2024/6pv8_20488.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/09_2024/6pv8_20488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/09_2024/6pv8_20488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/09_2024/6pv8_20488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/09_2024/6pv8_20488.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv8_20488/09_2024/6pv8_20488.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Br 2 7.06 5 S 127 5.16 5 Na 1 4.78 5 C 13107 2.51 5 N 3094 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20051 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "C" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3126 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'P1M': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {' NA': 1, 'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'P1M': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.34, per 1000 atoms: 0.62 Number of scatterers: 20051 At special positions: 0 Unit cell: (115.92, 112.56, 201.6, 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) Br 2 34.99 S 127 16.00 Na 1 11.00 O 3720 8.00 N 3094 7.00 C 13107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 132 " - pdb=" SG CYS E 146 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.04 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS G 109 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS I 45 " - pdb=" SG CYS I 109 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG B 701 " - " ASN B 15 " " NAG B 702 " - " ASN B 72 " " NAG C 701 " - " ASN C 15 " " NAG C 702 " - " ASN C 72 " " NAG E 701 " - " ASN E 15 " " NAG E 702 " - " ASN E 72 " " NAG J 1 " - " ASN A 24 " " NAG K 1 " - " ASN A 141 " " NAG L 1 " - " ASN B 117 " " NAG M 1 " - " ASN B 145 " " NAG N 1 " - " ASN C 117 " " NAG O 1 " - " ASN C 145 " " NAG P 1 " - " ASN D 24 " " NAG Q 1 " - " ASN D 141 " " NAG R 1 " - " ASN E 117 " " NAG S 1 " - " ASN E 145 " Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 2.6 seconds 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 31 sheets defined 33.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.771A pdb=" N PHE A 12 " --> pdb=" O PHE A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 227 through 228 No H-bonds generated for 'chain 'A' and resid 227 through 228' Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.726A pdb=" N PHE A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 263 removed outlier: 3.799A pdb=" N LEU A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 removed outlier: 3.888A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.858A pdb=" N THR A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 463 removed outlier: 3.559A pdb=" N ALA A 441 " --> pdb=" O TRP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.649A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 14 " --> pdb=" O MET B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 5.534A pdb=" N ILE B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 241 through 264 removed outlier: 3.867A pdb=" N LEU B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.715A pdb=" N VAL B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 401 through 457 removed outlier: 4.036A pdb=" N GLU B 405 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.593A pdb=" N LEU C 9 " --> pdb=" O ALA C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.588A pdb=" N ILE C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.553A pdb=" N ASN C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 241 through 264 removed outlier: 3.758A pdb=" N LEU C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 298 removed outlier: 3.822A pdb=" N CYS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 401 through 457 removed outlier: 4.495A pdb=" N GLU C 405 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.756A pdb=" N PHE D 12 " --> pdb=" O PHE D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.589A pdb=" N ASP D 71 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.699A pdb=" N TYR D 233 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 263 removed outlier: 3.852A pdb=" N LEU D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 299 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.943A pdb=" N THR D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 removed outlier: 3.687A pdb=" N ARG D 321 " --> pdb=" O ASN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 464 removed outlier: 3.555A pdb=" N ALA D 441 " --> pdb=" O TRP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.626A pdb=" N LEU D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.621A pdb=" N LYS E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.569A pdb=" N ARG E 88 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 89 " --> pdb=" O ALA E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 211 through 218 removed outlier: 3.606A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 230 removed outlier: 4.145A pdb=" N ILE E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 264 removed outlier: 3.872A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 298 removed outlier: 3.896A pdb=" N VAL E 298 " --> pdb=" O CYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 removed outlier: 3.705A pdb=" N PHE E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 324 removed outlier: 3.851A pdb=" N THR E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 457 removed outlier: 3.789A pdb=" N GLU E 405 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 407 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.596A pdb=" N ASP F 109 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 110' Processing helix chain 'H' and resid 81 through 84 removed outlier: 4.113A pdb=" N LYS H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.532A pdb=" N ASP H 109 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'I' and resid 100 through 104 removed outlier: 4.116A pdb=" N ALA I 104 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.562A pdb=" N VAL A 80 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.562A pdb=" N VAL A 80 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE A 49 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS A 42 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN A 53 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN A 61 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 30 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 146 removed outlier: 7.281A pdb=" N TYR A 205 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 146 Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 85 removed outlier: 4.476A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 126 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 85 removed outlier: 4.476A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 46 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ASN B 57 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 44 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N TRP B 59 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA B 42 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LYS B 61 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER B 40 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU B 63 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLN B 38 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N THR B 65 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N LYS B 36 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 96 removed outlier: 7.593A pdb=" N ILE B 206 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 113 through 114 removed outlier: 5.201A pdb=" N THR C 65 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER C 34 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE C 33 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 163 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE C 35 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.358A pdb=" N LEU C 44 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN C 57 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 46 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 96 removed outlier: 7.278A pdb=" N ILE C 206 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 110 Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 110 removed outlier: 7.075A pdb=" N ILE D 49 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS D 42 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ASN D 53 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 139 through 147 removed outlier: 7.192A pdb=" N TYR D 205 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 147 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.966A pdb=" N ALA E 126 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.689A pdb=" N SER E 46 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN E 57 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU E 44 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N TRP E 59 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA E 42 " --> pdb=" O TRP E 59 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS E 61 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER E 40 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLU E 63 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLN E 38 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N THR E 65 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N LYS E 36 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 33 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL E 163 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 35 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 94 through 96 removed outlier: 5.445A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 199 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE E 206 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 94 through 96 removed outlier: 5.445A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 199 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AC4, first strand: chain 'F' and resid 29 through 30 removed outlier: 6.824A pdb=" N LEU F 53 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL F 69 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 29 through 30 Processing sheet with id=AC6, first strand: chain 'G' and resid 27 through 29 Processing sheet with id=AC7, first strand: chain 'G' and resid 32 through 34 removed outlier: 3.536A pdb=" N MET G 33 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU G 126 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN G 58 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG G 67 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AC9, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.720A pdb=" N LEU H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL H 69 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 29 through 30 Processing sheet with id=AD2, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AD3, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.061A pdb=" N GLN I 58 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG I 67 " --> pdb=" O GLN I 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 32 through 34 removed outlier: 3.566A pdb=" N THR I 118 " --> pdb=" O GLN I 111 " (cutoff:3.500A) 959 hydrogen bonds defined for protein. 2703 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: 6.80 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5951 1.36 - 1.50: 5903 1.50 - 1.64: 8509 1.64 - 1.78: 1 1.78 - 1.92: 207 Bond restraints: 20571 Sorted by residual: bond pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.332 1.583 -0.252 1.34e-02 5.57e+03 3.52e+02 bond pdb=" C3 P1M D 701 " pdb=" N8 P1M D 701 " ideal model delta sigma weight residual 1.457 1.530 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C3 P1M A 701 " pdb=" N8 P1M A 701 " ideal model delta sigma weight residual 1.457 1.529 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N ASN C 117 " pdb=" CA ASN C 117 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.18e-02 7.18e+03 1.23e+01 bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.96e+00 ... (remaining 20566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 27216 2.65 - 5.31: 716 5.31 - 7.96: 120 7.96 - 10.62: 18 10.62 - 13.27: 11 Bond angle restraints: 28081 Sorted by residual: angle pdb=" O LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 121.31 109.06 12.25 8.50e-01 1.38e+00 2.08e+02 angle pdb=" C LEU A 234 " pdb=" N PRO A 235 " pdb=" CA PRO A 235 " ideal model delta sigma weight residual 119.78 133.05 -13.27 1.03e+00 9.43e-01 1.66e+02 angle pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 119.19 130.10 -10.91 9.50e-01 1.11e+00 1.32e+02 angle pdb=" N TYR H 122 " pdb=" CA TYR H 122 " pdb=" C TYR H 122 " ideal model delta sigma weight residual 109.81 120.06 -10.25 2.21e+00 2.05e-01 2.15e+01 angle pdb=" N TYR F 122 " pdb=" CA TYR F 122 " pdb=" C TYR F 122 " ideal model delta sigma weight residual 109.81 120.01 -10.20 2.21e+00 2.05e-01 2.13e+01 ... (remaining 28076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 12858 27.68 - 55.35: 329 55.35 - 83.03: 59 83.03 - 110.70: 48 110.70 - 138.38: 3 Dihedral angle restraints: 13297 sinusoidal: 6243 harmonic: 7054 Sorted by residual: dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CB CYS D 128 " pdb=" SG CYS D 128 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual 93.00 48.72 44.28 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 13294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3207 0.133 - 0.265: 155 0.265 - 0.398: 23 0.398 - 0.530: 9 0.530 - 0.663: 1 Chirality restraints: 3395 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.52e+01 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.26 0.14 2.00e-02 2.50e+03 4.94e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.62e+01 ... (remaining 3392 not shown) Planarity restraints: 3335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " -0.269 2.00e-02 2.50e+03 2.26e-01 6.37e+02 pdb=" C7 NAG C 702 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " 0.381 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.187 2.00e-02 2.50e+03 1.55e-01 3.01e+02 pdb=" C7 NAG N 2 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.137 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.253 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 234 " 0.024 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C LEU A 234 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU A 234 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO A 235 " 0.022 2.00e-02 2.50e+03 ... (remaining 3332 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 141 2.63 - 3.19: 15928 3.19 - 3.76: 28623 3.76 - 4.33: 38330 4.33 - 4.90: 64291 Nonbonded interactions: 147313 Sorted by model distance: nonbonded pdb=" O GLY D 239 " pdb=" OE2 GLU E 241 " model vdw 2.057 3.040 nonbonded pdb=" O3 NAG C 702 " pdb=" O7 NAG C 702 " model vdw 2.109 3.040 nonbonded pdb=" NH1 ARG E 188 " pdb=" OD2 ASP E 204 " model vdw 2.113 3.120 nonbonded pdb=" OE2 GLU C 159 " pdb=" NH1 ARG D 79 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASP I 103 " pdb=" OH TYR I 107 " model vdw 2.306 3.040 ... (remaining 147308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 4 through 459 or resid 701 through 712)) selection = chain 'C' selection = (chain 'E' and (resid 4 through 459 or resid 701 through 712)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.070 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.006 0.252 20571 Z= 0.400 Angle : 1.067 13.271 28081 Z= 0.540 Chirality : 0.071 0.663 3395 Planarity : 0.009 0.226 3319 Dihedral : 14.130 138.376 8694 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.69 % Allowed : 3.45 % Favored : 95.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.44 % 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: -2.83 (0.15), residues: 2351 helix: -1.69 (0.15), residues: 747 sheet: -0.68 (0.21), residues: 568 loop : -2.69 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 153 HIS 0.004 0.001 HIS B 416 PHE 0.031 0.002 PHE G 119 TYR 0.026 0.003 TYR E 97 ARG 0.020 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 645 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7745 (p0) cc_final: 0.7499 (p0) REVERT: B 66 ASP cc_start: 0.8445 (t0) cc_final: 0.8236 (t0) REVERT: B 74 SER cc_start: 0.8438 (p) cc_final: 0.8183 (t) REVERT: B 182 ILE cc_start: 0.8509 (pt) cc_final: 0.7206 (pt) REVERT: B 206 ILE cc_start: 0.9094 (pt) cc_final: 0.8573 (mt) REVERT: B 216 ILE cc_start: 0.9191 (tp) cc_final: 0.8713 (tt) REVERT: B 219 ILE cc_start: 0.7580 (mm) cc_final: 0.7360 (mm) REVERT: B 326 MET cc_start: 0.8607 (mmm) cc_final: 0.8223 (mmm) REVERT: C 7 GLU cc_start: 0.6277 (tt0) cc_final: 0.6021 (tt0) REVERT: C 70 THR cc_start: 0.7026 (p) cc_final: 0.6822 (p) REVERT: D 325 MET cc_start: 0.6970 (mmm) cc_final: 0.6711 (mmp) REVERT: E 38 GLN cc_start: 0.8506 (tm130) cc_final: 0.8168 (tt0) REVERT: E 249 VAL cc_start: 0.8853 (t) cc_final: 0.8556 (m) REVERT: F 110 SER cc_start: 0.7752 (m) cc_final: 0.7431 (t) REVERT: G 95 THR cc_start: 0.8568 (m) cc_final: 0.8042 (p) REVERT: G 112 TRP cc_start: 0.6988 (t-100) cc_final: 0.6416 (t-100) REVERT: G 117 LEU cc_start: 0.8086 (tp) cc_final: 0.7852 (tp) REVERT: H 78 ASN cc_start: 0.7792 (m-40) cc_final: 0.7526 (m-40) REVERT: I 79 VAL cc_start: 0.7878 (t) cc_final: 0.7673 (t) REVERT: I 95 THR cc_start: 0.8598 (m) cc_final: 0.8217 (p) outliers start: 15 outliers final: 6 residues processed: 658 average time/residue: 0.3065 time to fit residues: 304.1403 Evaluate side-chains 382 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 376 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain C residue 153 TRP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.9980 chunk 175 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 135 optimal weight: 0.0870 chunk 210 optimal weight: 0.0170 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 427 GLN A 428 ASN B 98 ASN B 144 GLN C 111 ASN C 143 GLN C 416 HIS D 16 ASN D 191 ASN E 43 GLN F 25 GLN H 25 GLN H 81 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20571 Z= 0.173 Angle : 0.672 10.518 28081 Z= 0.327 Chirality : 0.046 0.376 3395 Planarity : 0.005 0.048 3319 Dihedral : 12.802 130.064 4167 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.81 % Allowed : 12.24 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2351 helix: 0.63 (0.19), residues: 734 sheet: -0.38 (0.21), residues: 589 loop : -2.27 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 60 HIS 0.008 0.001 HIS C 416 PHE 0.016 0.001 PHE B 174 TYR 0.021 0.001 TYR F 122 ARG 0.007 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 427 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 SER cc_start: 0.9390 (t) cc_final: 0.9008 (m) REVERT: B 82 LEU cc_start: 0.8785 (tm) cc_final: 0.8441 (tp) REVERT: B 206 ILE cc_start: 0.8782 (pt) cc_final: 0.8525 (mt) REVERT: B 216 ILE cc_start: 0.9034 (tp) cc_final: 0.8775 (tt) REVERT: B 219 ILE cc_start: 0.7573 (mm) cc_final: 0.7245 (mm) REVERT: B 326 MET cc_start: 0.8673 (mmm) cc_final: 0.8276 (mmm) REVERT: B 402 ASP cc_start: 0.5315 (p0) cc_final: 0.3959 (t70) REVERT: B 446 MET cc_start: 0.7543 (tmm) cc_final: 0.5911 (ttt) REVERT: E 82 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8390 (tp) REVERT: F 62 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7677 (mmtm) REVERT: F 110 SER cc_start: 0.8040 (m) cc_final: 0.7738 (t) REVERT: G 95 THR cc_start: 0.8488 (m) cc_final: 0.8099 (p) REVERT: G 112 TRP cc_start: 0.7030 (t-100) cc_final: 0.6092 (t-100) REVERT: H 117 SER cc_start: 0.9088 (p) cc_final: 0.8755 (m) REVERT: I 33 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7832 (ptm) REVERT: I 95 THR cc_start: 0.8691 (m) cc_final: 0.8173 (p) outliers start: 61 outliers final: 39 residues processed: 467 average time/residue: 0.2818 time to fit residues: 207.2541 Evaluate side-chains 381 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 340 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 175 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 187 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN C 4 ASN C 192 ASN D 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20571 Z= 0.246 Angle : 0.666 9.778 28081 Z= 0.325 Chirality : 0.047 0.372 3395 Planarity : 0.005 0.058 3319 Dihedral : 11.468 122.729 4158 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.54 % Allowed : 14.26 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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 (0.17), residues: 2351 helix: 1.37 (0.20), residues: 732 sheet: -0.28 (0.21), residues: 589 loop : -2.10 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 311 HIS 0.003 0.001 HIS B 300 PHE 0.020 0.001 PHE D 283 TYR 0.024 0.002 TYR F 128 ARG 0.006 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 355 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 VAL cc_start: 0.8719 (t) cc_final: 0.8478 (t) REVERT: B 82 LEU cc_start: 0.8840 (tm) cc_final: 0.8534 (tp) REVERT: B 206 ILE cc_start: 0.8823 (pt) cc_final: 0.8521 (mt) REVERT: B 216 ILE cc_start: 0.9033 (tp) cc_final: 0.8822 (tt) REVERT: B 219 ILE cc_start: 0.7608 (mm) cc_final: 0.7234 (mm) REVERT: B 326 MET cc_start: 0.8707 (mmm) cc_final: 0.8303 (mmm) REVERT: C 38 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7736 (tt0) REVERT: C 218 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7506 (tt) REVERT: C 276 LYS cc_start: 0.7356 (ttmt) cc_final: 0.6548 (tptt) REVERT: E 38 GLN cc_start: 0.8737 (tm130) cc_final: 0.8321 (tt0) REVERT: E 82 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8592 (tp) REVERT: F 62 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7799 (mmtm) REVERT: G 95 THR cc_start: 0.8530 (m) cc_final: 0.8125 (p) REVERT: G 112 TRP cc_start: 0.7466 (t-100) cc_final: 0.6762 (t-100) REVERT: I 33 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7772 (ptm) REVERT: I 95 THR cc_start: 0.8786 (m) cc_final: 0.8333 (p) outliers start: 77 outliers final: 54 residues processed: 406 average time/residue: 0.2731 time to fit residues: 177.4912 Evaluate side-chains 388 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 331 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 86 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN B 299 HIS C 4 ASN D 317 ASN H 24 GLN H 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20571 Z= 0.183 Angle : 0.614 9.435 28081 Z= 0.298 Chirality : 0.045 0.355 3395 Planarity : 0.004 0.048 3319 Dihedral : 10.384 117.647 4158 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.91 % Allowed : 15.73 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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: -0.42 (0.17), residues: 2351 helix: 1.82 (0.20), residues: 727 sheet: -0.28 (0.22), residues: 562 loop : -1.84 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 311 HIS 0.003 0.001 HIS E 306 PHE 0.017 0.001 PHE D 283 TYR 0.030 0.001 TYR E 234 ARG 0.003 0.000 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 355 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7253 (mt-10) REVERT: A 233 TYR cc_start: 0.7017 (t80) cc_final: 0.6767 (t80) REVERT: B 38 GLN cc_start: 0.7794 (pp30) cc_final: 0.7475 (pp30) REVERT: B 82 LEU cc_start: 0.8751 (tm) cc_final: 0.8522 (tp) REVERT: B 162 MET cc_start: 0.8534 (mmm) cc_final: 0.8238 (mmt) REVERT: B 206 ILE cc_start: 0.8778 (pt) cc_final: 0.8575 (mt) REVERT: B 216 ILE cc_start: 0.9019 (tp) cc_final: 0.8804 (tt) REVERT: B 219 ILE cc_start: 0.7534 (mm) cc_final: 0.7145 (mm) REVERT: B 326 MET cc_start: 0.8698 (mmm) cc_final: 0.8282 (mmm) REVERT: B 446 MET cc_start: 0.7484 (tmm) cc_final: 0.6045 (ttt) REVERT: C 38 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7692 (tt0) REVERT: C 276 LYS cc_start: 0.7422 (ttmt) cc_final: 0.6569 (tptt) REVERT: D 191 ASN cc_start: 0.7026 (t0) cc_final: 0.6718 (t0) REVERT: D 435 ASP cc_start: 0.7226 (m-30) cc_final: 0.6769 (t0) REVERT: E 38 GLN cc_start: 0.8696 (tm130) cc_final: 0.8356 (tt0) REVERT: E 82 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8392 (tp) REVERT: F 22 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7197 (mm110) REVERT: F 84 LYS cc_start: 0.8192 (tptp) cc_final: 0.7176 (pttp) REVERT: G 95 THR cc_start: 0.8605 (m) cc_final: 0.8218 (p) REVERT: G 112 TRP cc_start: 0.7344 (t-100) cc_final: 0.6645 (t-100) REVERT: H 48 PHE cc_start: 0.7005 (t80) cc_final: 0.6619 (t80) REVERT: I 95 THR cc_start: 0.8779 (m) cc_final: 0.8378 (p) outliers start: 85 outliers final: 56 residues processed: 410 average time/residue: 0.2748 time to fit residues: 180.3599 Evaluate side-chains 391 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 334 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 8.9990 chunk 127 optimal weight: 0.0370 chunk 3 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 92 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 201 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN E 4 ASN E 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20571 Z= 0.164 Angle : 0.605 14.982 28081 Z= 0.290 Chirality : 0.045 0.348 3395 Planarity : 0.004 0.051 3319 Dihedral : 9.866 113.223 4158 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.17 % Allowed : 17.02 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2351 helix: 1.92 (0.20), residues: 743 sheet: -0.20 (0.22), residues: 562 loop : -1.74 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 311 HIS 0.002 0.000 HIS B 300 PHE 0.016 0.001 PHE D 283 TYR 0.021 0.001 TYR E 234 ARG 0.003 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 355 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7326 (mt-10) REVERT: A 233 TYR cc_start: 0.6968 (t80) cc_final: 0.6705 (t80) REVERT: B 38 GLN cc_start: 0.7778 (pp30) cc_final: 0.7508 (pp30) REVERT: B 162 MET cc_start: 0.8544 (mmm) cc_final: 0.8119 (mmt) REVERT: B 216 ILE cc_start: 0.8998 (tp) cc_final: 0.8770 (tt) REVERT: B 219 ILE cc_start: 0.7539 (mm) cc_final: 0.7170 (mm) REVERT: B 308 MET cc_start: 0.7018 (mmm) cc_final: 0.6724 (mmm) REVERT: B 326 MET cc_start: 0.8708 (mmm) cc_final: 0.8303 (mmm) REVERT: B 446 MET cc_start: 0.7494 (tmm) cc_final: 0.6052 (ttt) REVERT: C 38 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7724 (tt0) REVERT: C 76 TYR cc_start: 0.7494 (m-80) cc_final: 0.7010 (m-10) REVERT: C 276 LYS cc_start: 0.7439 (ttmt) cc_final: 0.6610 (tptt) REVERT: D 191 ASN cc_start: 0.6943 (t0) cc_final: 0.6695 (t0) REVERT: D 435 ASP cc_start: 0.7147 (m-30) cc_final: 0.6709 (t0) REVERT: E 38 GLN cc_start: 0.8645 (tm130) cc_final: 0.8354 (tt0) REVERT: E 82 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8471 (tp) REVERT: E 282 MET cc_start: 0.8177 (tpp) cc_final: 0.7833 (ttm) REVERT: F 84 LYS cc_start: 0.8233 (tptp) cc_final: 0.7170 (pttp) REVERT: G 95 THR cc_start: 0.8647 (m) cc_final: 0.8262 (p) REVERT: G 112 TRP cc_start: 0.7253 (t-100) cc_final: 0.6424 (t-100) REVERT: H 48 PHE cc_start: 0.7024 (t80) cc_final: 0.6599 (t80) REVERT: I 95 THR cc_start: 0.8740 (m) cc_final: 0.8397 (p) outliers start: 69 outliers final: 52 residues processed: 403 average time/residue: 0.2851 time to fit residues: 183.8984 Evaluate side-chains 394 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 341 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20571 Z= 0.248 Angle : 0.653 11.608 28081 Z= 0.315 Chirality : 0.047 0.345 3395 Planarity : 0.004 0.052 3319 Dihedral : 9.611 110.499 4158 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.77 % Allowed : 17.07 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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: -0.17 (0.18), residues: 2351 helix: 2.06 (0.20), residues: 724 sheet: -0.18 (0.21), residues: 583 loop : -1.70 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 311 HIS 0.005 0.001 HIS B 300 PHE 0.019 0.002 PHE D 283 TYR 0.017 0.002 TYR F 128 ARG 0.003 0.000 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 342 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7330 (mt-10) REVERT: A 14 ASP cc_start: 0.8272 (p0) cc_final: 0.7868 (p0) REVERT: A 233 TYR cc_start: 0.7112 (t80) cc_final: 0.6901 (t80) REVERT: B 38 GLN cc_start: 0.7853 (pp30) cc_final: 0.7603 (pp30) REVERT: B 162 MET cc_start: 0.8557 (mmm) cc_final: 0.8245 (mmt) REVERT: B 216 ILE cc_start: 0.9094 (tp) cc_final: 0.8855 (tt) REVERT: B 219 ILE cc_start: 0.7540 (mm) cc_final: 0.7137 (mm) REVERT: B 308 MET cc_start: 0.7226 (mmm) cc_final: 0.6948 (mmm) REVERT: B 326 MET cc_start: 0.8729 (mmm) cc_final: 0.8351 (mmm) REVERT: C 183 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7407 (t) REVERT: C 276 LYS cc_start: 0.7659 (ttmt) cc_final: 0.6740 (tptt) REVERT: C 422 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7112 (mp0) REVERT: D 50 MET cc_start: 0.8021 (tmm) cc_final: 0.7799 (ttp) REVERT: D 191 ASN cc_start: 0.7447 (t0) cc_final: 0.7080 (t0) REVERT: D 435 ASP cc_start: 0.7254 (m-30) cc_final: 0.6802 (t0) REVERT: E 38 GLN cc_start: 0.8716 (tm130) cc_final: 0.8404 (tt0) REVERT: F 84 LYS cc_start: 0.8278 (tptp) cc_final: 0.7253 (pttp) REVERT: G 95 THR cc_start: 0.8708 (m) cc_final: 0.8295 (p) REVERT: G 112 TRP cc_start: 0.7557 (t-100) cc_final: 0.6721 (t-100) REVERT: I 95 THR cc_start: 0.8774 (m) cc_final: 0.8503 (p) REVERT: I 99 MET cc_start: 0.7140 (tpp) cc_final: 0.6393 (tpp) outliers start: 82 outliers final: 64 residues processed: 401 average time/residue: 0.2724 time to fit residues: 175.0870 Evaluate side-chains 394 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 329 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 97 TYR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 86 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 0.4980 chunk 163 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 136 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20571 Z= 0.159 Angle : 0.598 10.800 28081 Z= 0.288 Chirality : 0.044 0.330 3395 Planarity : 0.004 0.050 3319 Dihedral : 9.233 106.570 4158 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.04 % Allowed : 18.12 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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: 0.02 (0.18), residues: 2351 helix: 2.18 (0.20), residues: 736 sheet: -0.05 (0.22), residues: 578 loop : -1.61 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 311 HIS 0.004 0.000 HIS I 55 PHE 0.015 0.001 PHE D 283 TYR 0.024 0.001 TYR C 76 ARG 0.006 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 341 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7329 (mt-10) REVERT: A 14 ASP cc_start: 0.8228 (p0) cc_final: 0.7837 (p0) REVERT: A 233 TYR cc_start: 0.6969 (t80) cc_final: 0.6703 (t80) REVERT: A 256 LEU cc_start: 0.8270 (tp) cc_final: 0.7972 (tp) REVERT: B 38 GLN cc_start: 0.7833 (pp30) cc_final: 0.7611 (pp30) REVERT: B 41 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9127 (tp) REVERT: B 162 MET cc_start: 0.8555 (mmm) cc_final: 0.8059 (mmt) REVERT: B 216 ILE cc_start: 0.9014 (tp) cc_final: 0.8779 (tt) REVERT: B 219 ILE cc_start: 0.7492 (mm) cc_final: 0.7070 (mm) REVERT: B 308 MET cc_start: 0.7236 (mmm) cc_final: 0.6999 (mmm) REVERT: B 326 MET cc_start: 0.8701 (mmm) cc_final: 0.8328 (mmm) REVERT: B 446 MET cc_start: 0.7360 (tmm) cc_final: 0.5952 (ttt) REVERT: C 183 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.7364 (t) REVERT: C 276 LYS cc_start: 0.7516 (ttmt) cc_final: 0.6602 (tptt) REVERT: C 422 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7063 (mp0) REVERT: D 50 MET cc_start: 0.7951 (tmm) cc_final: 0.7697 (ttp) REVERT: D 191 ASN cc_start: 0.7206 (t0) cc_final: 0.6991 (t0) REVERT: D 435 ASP cc_start: 0.7170 (m-30) cc_final: 0.6722 (t0) REVERT: E 38 GLN cc_start: 0.8664 (tm130) cc_final: 0.8410 (tt0) REVERT: E 82 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8553 (tp) REVERT: F 37 VAL cc_start: 0.7787 (m) cc_final: 0.7344 (p) REVERT: F 128 TYR cc_start: 0.7841 (m-10) cc_final: 0.7554 (m-10) REVERT: G 95 THR cc_start: 0.8676 (m) cc_final: 0.8262 (p) REVERT: G 112 TRP cc_start: 0.7291 (t-100) cc_final: 0.6507 (t-100) REVERT: H 48 PHE cc_start: 0.7091 (t80) cc_final: 0.6537 (t80) REVERT: H 99 TYR cc_start: 0.8415 (m-80) cc_final: 0.8179 (m-80) REVERT: I 95 THR cc_start: 0.8771 (m) cc_final: 0.8468 (p) REVERT: I 99 MET cc_start: 0.7111 (tpp) cc_final: 0.6394 (tpp) outliers start: 66 outliers final: 53 residues processed: 390 average time/residue: 0.3234 time to fit residues: 204.4929 Evaluate side-chains 385 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 329 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 chunk 203 optimal weight: 0.0870 chunk 214 optimal weight: 7.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 428 ASN H 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20571 Z= 0.209 Angle : 0.627 11.663 28081 Z= 0.302 Chirality : 0.045 0.336 3395 Planarity : 0.004 0.052 3319 Dihedral : 9.039 104.442 4158 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.54 % Allowed : 18.35 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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 (0.18), residues: 2351 helix: 2.27 (0.20), residues: 722 sheet: -0.04 (0.22), residues: 578 loop : -1.62 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 311 HIS 0.004 0.001 HIS E 416 PHE 0.024 0.001 PHE B 412 TYR 0.024 0.001 TYR C 76 ARG 0.005 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 341 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8265 (p0) cc_final: 0.7915 (p0) REVERT: A 111 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8245 (mttm) REVERT: A 233 TYR cc_start: 0.7056 (t80) cc_final: 0.6721 (t80) REVERT: B 38 GLN cc_start: 0.7885 (pp30) cc_final: 0.7596 (pp30) REVERT: B 162 MET cc_start: 0.8558 (mmm) cc_final: 0.8237 (mmt) REVERT: B 216 ILE cc_start: 0.9076 (tp) cc_final: 0.8833 (tt) REVERT: B 219 ILE cc_start: 0.7506 (mm) cc_final: 0.7075 (mm) REVERT: B 308 MET cc_start: 0.7286 (mmm) cc_final: 0.7032 (mmm) REVERT: B 326 MET cc_start: 0.8711 (mmm) cc_final: 0.8377 (mmm) REVERT: B 446 MET cc_start: 0.7398 (tmm) cc_final: 0.6038 (ttt) REVERT: C 183 VAL cc_start: 0.7639 (OUTLIER) cc_final: 0.7350 (t) REVERT: C 276 LYS cc_start: 0.7593 (ttmt) cc_final: 0.6691 (tptt) REVERT: C 422 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7067 (mp0) REVERT: D 191 ASN cc_start: 0.7488 (t0) cc_final: 0.7181 (t0) REVERT: D 429 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7225 (tm-30) REVERT: D 435 ASP cc_start: 0.7222 (m-30) cc_final: 0.6756 (t0) REVERT: E 38 GLN cc_start: 0.8721 (tm130) cc_final: 0.8416 (tt0) REVERT: E 435 MET cc_start: 0.7299 (ttp) cc_final: 0.6997 (ttm) REVERT: G 95 THR cc_start: 0.8748 (m) cc_final: 0.8323 (p) REVERT: G 112 TRP cc_start: 0.7442 (t-100) cc_final: 0.6669 (t-100) REVERT: H 96 SER cc_start: 0.8741 (m) cc_final: 0.8431 (p) REVERT: H 99 TYR cc_start: 0.8350 (m-80) cc_final: 0.8130 (m-80) REVERT: I 95 THR cc_start: 0.8801 (m) cc_final: 0.8542 (p) outliers start: 77 outliers final: 67 residues processed: 393 average time/residue: 0.2837 time to fit residues: 177.1573 Evaluate side-chains 392 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 323 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20571 Z= 0.191 Angle : 0.614 10.932 28081 Z= 0.296 Chirality : 0.045 0.330 3395 Planarity : 0.004 0.051 3319 Dihedral : 8.845 102.368 4158 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.50 % Allowed : 18.58 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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: 0.09 (0.18), residues: 2351 helix: 2.36 (0.20), residues: 722 sheet: -0.05 (0.22), residues: 580 loop : -1.59 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 311 HIS 0.004 0.001 HIS E 416 PHE 0.024 0.001 PHE B 412 TYR 0.018 0.001 TYR C 76 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 339 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7374 (mt-10) REVERT: A 14 ASP cc_start: 0.8218 (p0) cc_final: 0.7935 (p0) REVERT: A 111 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8245 (mttm) REVERT: A 233 TYR cc_start: 0.7057 (t80) cc_final: 0.6726 (t80) REVERT: B 38 GLN cc_start: 0.7876 (pp30) cc_final: 0.7575 (pp30) REVERT: B 41 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9152 (tp) REVERT: B 162 MET cc_start: 0.8554 (mmm) cc_final: 0.8150 (mmt) REVERT: B 216 ILE cc_start: 0.9015 (tp) cc_final: 0.8744 (tt) REVERT: B 219 ILE cc_start: 0.7476 (mm) cc_final: 0.7123 (mm) REVERT: B 326 MET cc_start: 0.8704 (mmm) cc_final: 0.8407 (mmm) REVERT: C 183 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7313 (t) REVERT: C 276 LYS cc_start: 0.7544 (ttmt) cc_final: 0.6634 (tptt) REVERT: C 422 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7061 (mp0) REVERT: D 429 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7240 (tm-30) REVERT: D 435 ASP cc_start: 0.7206 (m-30) cc_final: 0.6774 (t0) REVERT: E 38 GLN cc_start: 0.8718 (tm130) cc_final: 0.8352 (tt0) REVERT: E 133 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7365 (pttp) REVERT: E 435 MET cc_start: 0.7257 (ttp) cc_final: 0.7021 (ttm) REVERT: G 95 THR cc_start: 0.8773 (m) cc_final: 0.8353 (p) REVERT: G 112 TRP cc_start: 0.7410 (t-100) cc_final: 0.6631 (t-100) REVERT: H 96 SER cc_start: 0.8757 (m) cc_final: 0.8447 (p) REVERT: I 95 THR cc_start: 0.8790 (m) cc_final: 0.8538 (p) REVERT: I 100 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7557 (tp30) REVERT: I 115 ASN cc_start: 0.8176 (t0) cc_final: 0.7906 (m110) outliers start: 76 outliers final: 64 residues processed: 392 average time/residue: 0.2811 time to fit residues: 175.8501 Evaluate side-chains 399 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 332 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 86 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 153 optimal weight: 0.4980 chunk 231 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 184 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 22 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20571 Z= 0.168 Angle : 0.605 11.038 28081 Z= 0.290 Chirality : 0.044 0.323 3395 Planarity : 0.004 0.051 3319 Dihedral : 8.605 98.754 4158 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.17 % Allowed : 19.32 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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 (0.18), residues: 2351 helix: 2.43 (0.20), residues: 722 sheet: 0.00 (0.22), residues: 580 loop : -1.58 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 311 HIS 0.003 0.000 HIS I 55 PHE 0.025 0.001 PHE B 412 TYR 0.016 0.001 TYR C 76 ARG 0.003 0.000 ARG C 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 335 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7361 (mt-10) REVERT: A 14 ASP cc_start: 0.8170 (p0) cc_final: 0.7924 (p0) REVERT: A 37 MET cc_start: 0.8403 (tpp) cc_final: 0.8099 (ttt) REVERT: A 111 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8015 (mttm) REVERT: A 233 TYR cc_start: 0.7031 (t80) cc_final: 0.6725 (t80) REVERT: B 41 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9159 (tp) REVERT: B 162 MET cc_start: 0.8547 (mmm) cc_final: 0.8111 (mmt) REVERT: B 216 ILE cc_start: 0.8977 (tp) cc_final: 0.8735 (tt) REVERT: B 219 ILE cc_start: 0.7561 (mm) cc_final: 0.7152 (mm) REVERT: B 251 LEU cc_start: 0.8222 (tt) cc_final: 0.7663 (mt) REVERT: B 326 MET cc_start: 0.8644 (mmm) cc_final: 0.8380 (mmm) REVERT: B 446 MET cc_start: 0.7368 (tmm) cc_final: 0.5885 (ttt) REVERT: C 183 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7327 (t) REVERT: C 276 LYS cc_start: 0.7470 (ttmt) cc_final: 0.6588 (tptt) REVERT: C 422 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7065 (mp0) REVERT: D 91 VAL cc_start: 0.8589 (t) cc_final: 0.8337 (m) REVERT: D 429 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7203 (tm-30) REVERT: D 435 ASP cc_start: 0.7191 (m-30) cc_final: 0.6756 (t0) REVERT: E 38 GLN cc_start: 0.8662 (tm130) cc_final: 0.8348 (tt0) REVERT: E 82 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 133 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7265 (pttp) REVERT: G 33 MET cc_start: 0.6872 (ppp) cc_final: 0.6606 (ppp) REVERT: G 95 THR cc_start: 0.8805 (m) cc_final: 0.8389 (p) REVERT: G 112 TRP cc_start: 0.7336 (t-100) cc_final: 0.6523 (t-100) REVERT: H 79 TYR cc_start: 0.8038 (m-80) cc_final: 0.7615 (m-80) REVERT: H 96 SER cc_start: 0.8733 (m) cc_final: 0.8475 (p) REVERT: H 99 TYR cc_start: 0.8284 (m-80) cc_final: 0.8043 (m-80) REVERT: I 95 THR cc_start: 0.8779 (m) cc_final: 0.8494 (p) REVERT: I 99 MET cc_start: 0.7190 (tpp) cc_final: 0.6334 (tpp) REVERT: I 115 ASN cc_start: 0.8179 (t0) cc_final: 0.7864 (m110) outliers start: 69 outliers final: 64 residues processed: 382 average time/residue: 0.2776 time to fit residues: 169.4326 Evaluate side-chains 394 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 326 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 122 TYR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 86 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 169 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 184 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.147010 restraints weight = 26803.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.140813 restraints weight = 44957.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.140450 restraints weight = 35605.775| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20571 Z= 0.149 Angle : 0.584 11.150 28081 Z= 0.280 Chirality : 0.043 0.320 3395 Planarity : 0.004 0.051 3319 Dihedral : 8.316 94.470 4158 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.90 % Allowed : 19.87 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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: 0.26 (0.18), residues: 2351 helix: 2.53 (0.20), residues: 722 sheet: 0.10 (0.22), residues: 580 loop : -1.56 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 59 HIS 0.004 0.000 HIS B 306 PHE 0.025 0.001 PHE B 412 TYR 0.016 0.001 TYR C 76 ARG 0.003 0.000 ARG D 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4196.98 seconds wall clock time: 75 minutes 57.56 seconds (4557.56 seconds total)