Starting phenix.real_space_refine on Sun Sep 13 02:39:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_20488.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_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 { model { file = "/net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_20488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_20488.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_20488.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_20488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_20488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pv8_20488/09_2026/6pv8_20488.map" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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: 8 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 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: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 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: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 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: 8 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 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: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 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: 4.61, per 1000 atoms: 0.23 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: 2.08 Conformation dependent library (CDL) restraints added in 830.8 milliseconds 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: 0.53 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: 3.50 Time building geometry restraints manager: 2.60 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 - 14.34: 11037 14.34 - 28.69: 576 28.69 - 43.03: 170 43.03 - 57.38: 15 57.38 - 71.72: 7 Dihedral angle restraints: 11805 sinusoidal: 4751 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 11802 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 712) selection = chain 'C' selection = (chain 'E' and resid 4 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: 2.620 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.850 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 20626 Z= 0.344 Angle : 1.085 13.271 28235 Z= 0.544 Chirality : 0.071 0.663 3395 Planarity : 0.009 0.226 3319 Dihedral : 9.812 71.720 7202 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.020 0.001 ARG A 6 TYR 0.026 0.003 TYR E 97 PHE 0.031 0.002 PHE G 119 TRP 0.046 0.002 TRP E 153 HIS 0.004 0.001 HIS B 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.34 (20571) covalent geometry : angle 1.06742 / 0.54 (28081) SS BOND : bond 0.00792 / 0.47 ( 11) SS BOND : angle 1.60536 / 1.03 ( 22) hydrogen bonds : bond 0.16994 / 11.31 ( 858) hydrogen bonds : angle 6.27268 / 4.30 ( 2703) link_ALPHA1-3 : bond 0.00662 / 0.44 ( 5) link_ALPHA1-3 : angle 2.32867 / 1.26 ( 15) link_ALPHA1-6 : bond 0.00598 / 0.34 ( 5) link_ALPHA1-6 : angle 1.68350 / 1.00 ( 15) link_BETA1-4 : bond 0.00838 / 0.52 ( 18) link_BETA1-4 : angle 2.50988 / 1.61 ( 54) link_NAG-ASN : bond 0.01106 / 0.71 ( 16) link_NAG-ASN : angle 3.95768 / 2.96 ( 48) *********************** 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 to be fit. rotamer outliers: 15 poor density : 645 time to evaluate : 0.766 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: 0.1458 time to fit residues: 147.7647 Evaluate side-chains 382 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 376 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151827 restraints weight = 26364.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.150330 restraints weight = 47824.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.150497 restraints weight = 47630.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.150248 restraints weight = 31609.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150488 restraints weight = 27717.147| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20626 Z= 0.129 Angle : 0.684 10.220 28235 Z= 0.330 Chirality : 0.045 0.358 3395 Planarity : 0.005 0.049 3319 Dihedral : 5.807 58.363 2675 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.67 % Allowed : 12.47 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.17), residues: 2351 helix: 0.57 (0.19), residues: 734 sheet: -0.39 (0.21), residues: 589 loop : -2.28 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 6 TYR 0.021 0.001 TYR F 122 PHE 0.016 0.001 PHE E 441 TRP 0.015 0.001 TRP C 122 HIS 0.009 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (20571) covalent geometry : angle 0.66535 / 0.33 (28081) SS BOND : bond 0.00739 / 0.40 ( 11) SS BOND : angle 2.15045 / 1.31 ( 22) hydrogen bonds : bond 0.04832 / 3.14 ( 858) hydrogen bonds : angle 4.56993 / 3.11 ( 2703) link_ALPHA1-3 : bond 0.00975 / 0.55 ( 5) link_ALPHA1-3 : angle 1.86242 / 1.05 ( 15) link_ALPHA1-6 : bond 0.00687 / 0.38 ( 5) link_ALPHA1-6 : angle 1.45647 / 0.83 ( 15) link_BETA1-4 : bond 0.00498 / 0.32 ( 18) link_BETA1-4 : angle 1.79373 / 1.26 ( 54) link_NAG-ASN : bond 0.00487 / 0.31 ( 16) link_NAG-ASN : angle 2.93403 / 1.98 ( 48) *********************** 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 482 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 424 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.7981 (ttt) cc_final: 0.7773 (ttt) REVERT: A 148 SER cc_start: 0.9386 (t) cc_final: 0.9015 (m) REVERT: B 74 SER cc_start: 0.8354 (p) cc_final: 0.8149 (t) REVERT: B 82 LEU cc_start: 0.8803 (tm) cc_final: 0.8471 (tp) REVERT: B 206 ILE cc_start: 0.8819 (pt) cc_final: 0.8578 (mt) REVERT: B 216 ILE cc_start: 0.9055 (tp) cc_final: 0.8775 (tt) REVERT: B 219 ILE cc_start: 0.7578 (mm) cc_final: 0.7258 (mm) REVERT: B 326 MET cc_start: 0.8515 (mmm) cc_final: 0.8106 (mmm) REVERT: B 402 ASP cc_start: 0.4803 (p0) cc_final: 0.3778 (t70) REVERT: B 446 MET cc_start: 0.7506 (tmm) cc_final: 0.5885 (ttt) REVERT: E 82 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8343 (tp) REVERT: F 110 SER cc_start: 0.7779 (m) cc_final: 0.7452 (t) REVERT: G 95 THR cc_start: 0.8278 (m) cc_final: 0.7948 (p) REVERT: G 112 TRP cc_start: 0.7072 (t-100) cc_final: 0.6104 (t-100) REVERT: H 117 SER cc_start: 0.9121 (p) cc_final: 0.8742 (m) REVERT: I 33 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7578 (ptm) REVERT: I 95 THR cc_start: 0.8676 (m) cc_final: 0.8220 (p) outliers start: 58 outliers final: 39 residues processed: 464 average time/residue: 0.1314 time to fit residues: 98.0858 Evaluate side-chains 379 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 D residue 469 MET 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 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 129 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 203 optimal weight: 0.0270 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 GLN C 4 ASN C 192 ASN D 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.155910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147273 restraints weight = 26754.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142817 restraints weight = 40353.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.141237 restraints weight = 33640.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.141350 restraints weight = 31978.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141997 restraints weight = 26369.139| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20626 Z= 0.142 Angle : 0.652 9.662 28235 Z= 0.315 Chirality : 0.044 0.327 3395 Planarity : 0.005 0.059 3319 Dihedral : 5.441 59.212 2666 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.45 % Allowed : 14.08 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.17), residues: 2351 helix: 1.41 (0.20), residues: 732 sheet: -0.25 (0.21), residues: 589 loop : -2.08 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 6 TYR 0.024 0.001 TYR F 128 PHE 0.019 0.001 PHE D 283 TRP 0.017 0.001 TRP E 311 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (20571) covalent geometry : angle 0.63466 / 0.31 (28081) SS BOND : bond 0.00604 / 0.35 ( 11) SS BOND : angle 1.70149 / 1.04 ( 22) hydrogen bonds : bond 0.04549 / 2.94 ( 858) hydrogen bonds : angle 4.27479 / 2.92 ( 2703) link_ALPHA1-3 : bond 0.01158 / 0.66 ( 5) link_ALPHA1-3 : angle 1.77116 / 0.98 ( 15) link_ALPHA1-6 : bond 0.00654 / 0.35 ( 5) link_ALPHA1-6 : angle 1.33186 / 0.75 ( 15) link_BETA1-4 : bond 0.00492 / 0.32 ( 18) link_BETA1-4 : angle 1.66621 / 1.13 ( 54) link_NAG-ASN : bond 0.00602 / 0.35 ( 16) link_NAG-ASN : angle 2.93003 / 1.98 ( 48) *********************** 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 434 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 359 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8170 (p0) cc_final: 0.7829 (p0) REVERT: A 37 MET cc_start: 0.8143 (ttt) cc_final: 0.7899 (ttt) REVERT: A 97 VAL cc_start: 0.8697 (t) cc_final: 0.8456 (t) REVERT: B 74 SER cc_start: 0.8543 (p) cc_final: 0.8328 (t) REVERT: B 82 LEU cc_start: 0.8809 (tm) cc_final: 0.8526 (tp) REVERT: B 206 ILE cc_start: 0.8844 (pt) cc_final: 0.8582 (mt) REVERT: B 216 ILE cc_start: 0.8991 (tp) cc_final: 0.8783 (tt) REVERT: B 219 ILE cc_start: 0.7613 (mm) cc_final: 0.7218 (mm) REVERT: B 326 MET cc_start: 0.8714 (mmm) cc_final: 0.8297 (mmm) REVERT: C 38 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7721 (tt0) REVERT: C 276 LYS cc_start: 0.7290 (ttmt) cc_final: 0.6489 (tptt) REVERT: D 424 MET cc_start: 0.7521 (mmm) cc_final: 0.7312 (mmm) REVERT: D 435 ASP cc_start: 0.7302 (m-30) cc_final: 0.6844 (t0) REVERT: E 38 GLN cc_start: 0.8784 (tm130) cc_final: 0.8374 (tt0) REVERT: E 82 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8574 (tp) REVERT: G 95 THR cc_start: 0.8498 (m) cc_final: 0.8120 (p) REVERT: G 112 TRP cc_start: 0.7343 (t-100) cc_final: 0.6458 (t-100) REVERT: I 33 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7734 (ptm) REVERT: I 95 THR cc_start: 0.8780 (m) cc_final: 0.8327 (p) outliers start: 75 outliers final: 49 residues processed: 410 average time/residue: 0.1208 time to fit residues: 80.6253 Evaluate side-chains 385 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 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 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 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 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 86 SER Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS A 428 ASN B 299 HIS C 4 ASN C 20 ASN C 299 HIS D 298 HIS D 317 ASN E 4 ASN H 24 GLN H 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.146273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.137594 restraints weight = 27614.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131919 restraints weight = 39559.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130047 restraints weight = 37098.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129983 restraints weight = 37680.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130453 restraints weight = 31663.310| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20626 Z= 0.263 Angle : 0.811 9.330 28235 Z= 0.393 Chirality : 0.049 0.315 3395 Planarity : 0.005 0.058 3319 Dihedral : 5.927 55.243 2666 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.61 % Allowed : 15.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2351 helix: 1.29 (0.19), residues: 729 sheet: -0.63 (0.21), residues: 588 loop : -1.99 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 24 TYR 0.029 0.002 TYR C 97 PHE 0.023 0.002 PHE D 283 TRP 0.018 0.002 TRP B 180 HIS 0.009 0.002 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.26 (20571) covalent geometry : angle 0.79249 / 0.39 (28081) SS BOND : bond 0.00681 / 0.41 ( 11) SS BOND : angle 2.46637 / 1.66 ( 22) hydrogen bonds : bond 0.05532 / 3.58 ( 858) hydrogen bonds : angle 4.60443 / 3.15 ( 2703) link_ALPHA1-3 : bond 0.01105 / 0.64 ( 5) link_ALPHA1-3 : angle 1.86400 / 1.03 ( 15) link_ALPHA1-6 : bond 0.00622 / 0.32 ( 5) link_ALPHA1-6 : angle 1.35517 / 0.77 ( 15) link_BETA1-4 : bond 0.00642 / 0.40 ( 18) link_BETA1-4 : angle 1.98161 / 1.29 ( 54) link_NAG-ASN : bond 0.00519 / 0.37 ( 16) link_NAG-ASN : angle 3.23157 / 2.19 ( 48) *********************** 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 472 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 350 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7263 (mt-10) REVERT: A 37 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8197 (ttt) REVERT: A 233 TYR cc_start: 0.7406 (t80) cc_final: 0.7159 (t80) REVERT: B 38 GLN cc_start: 0.7884 (pp30) cc_final: 0.7563 (pp30) REVERT: B 137 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7855 (mttp) REVERT: B 162 MET cc_start: 0.8643 (mmm) cc_final: 0.8280 (mmt) REVERT: B 206 ILE cc_start: 0.8900 (pt) cc_final: 0.8635 (mt) REVERT: B 216 ILE cc_start: 0.9197 (tp) cc_final: 0.8951 (tt) REVERT: B 219 ILE cc_start: 0.7643 (mm) cc_final: 0.7247 (mm) REVERT: B 326 MET cc_start: 0.8763 (mmm) cc_final: 0.8381 (mmm) REVERT: B 446 MET cc_start: 0.7549 (tmm) cc_final: 0.6122 (ttt) REVERT: C 153 TRP cc_start: 0.8824 (OUTLIER) cc_final: 0.8497 (p90) REVERT: C 276 LYS cc_start: 0.7764 (ttmt) cc_final: 0.6795 (tptt) REVERT: D 435 ASP cc_start: 0.7528 (m-30) cc_final: 0.7104 (t0) REVERT: E 38 GLN cc_start: 0.8958 (tm130) cc_final: 0.8413 (tt0) REVERT: E 289 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8809 (tt) REVERT: G 72 THR cc_start: 0.8202 (m) cc_final: 0.7960 (m) REVERT: G 95 THR cc_start: 0.8694 (m) cc_final: 0.8231 (p) REVERT: G 112 TRP cc_start: 0.7877 (t-100) cc_final: 0.7104 (t-100) REVERT: I 95 THR cc_start: 0.8834 (m) cc_final: 0.8535 (p) outliers start: 122 outliers final: 87 residues processed: 435 average time/residue: 0.1245 time to fit residues: 88.1333 Evaluate side-chains 408 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 318 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 37 MET Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 148 SER 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 447 ILE 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 101 ASP 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 B residue 458 LEU Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 TRP 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 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 92 LEU Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 229 VAL 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 297 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 70 THR 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 114 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 232 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 289 ILE 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 E residue 312 VAL Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 THR 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 42 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 64 SER 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 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 89 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN A 428 ASN H 24 GLN H 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139978 restraints weight = 27025.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.136462 restraints weight = 34622.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.134859 restraints weight = 26003.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135062 restraints weight = 26230.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135126 restraints weight = 23786.281| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20626 Z= 0.143 Angle : 0.661 9.397 28235 Z= 0.318 Chirality : 0.044 0.278 3395 Planarity : 0.004 0.052 3319 Dihedral : 5.547 55.449 2666 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.77 % Allowed : 18.03 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.17), residues: 2351 helix: 1.75 (0.20), residues: 729 sheet: -0.50 (0.21), residues: 588 loop : -1.82 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 57 TYR 0.020 0.001 TYR F 122 PHE 0.018 0.001 PHE H 83 TRP 0.011 0.001 TRP C 153 HIS 0.003 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (20571) covalent geometry : angle 0.64342 / 0.31 (28081) SS BOND : bond 0.00548 / 0.31 ( 11) SS BOND : angle 2.10755 / 1.47 ( 22) hydrogen bonds : bond 0.04777 / 3.09 ( 858) hydrogen bonds : angle 4.27130 / 2.92 ( 2703) link_ALPHA1-3 : bond 0.00906 / 0.51 ( 5) link_ALPHA1-3 : angle 1.64060 / 0.93 ( 15) link_ALPHA1-6 : bond 0.00561 / 0.30 ( 5) link_ALPHA1-6 : angle 1.32108 / 0.74 ( 15) link_BETA1-4 : bond 0.00518 / 0.32 ( 18) link_BETA1-4 : angle 1.58778 / 1.07 ( 54) link_NAG-ASN : bond 0.00504 / 0.29 ( 16) link_NAG-ASN : angle 2.88439 / 1.93 ( 48) *********************** 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 422 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 340 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7311 (mt-10) REVERT: A 14 ASP cc_start: 0.8305 (p0) cc_final: 0.7905 (p0) REVERT: B 23 ILE cc_start: 0.8604 (pp) cc_final: 0.8152 (mt) REVERT: B 38 GLN cc_start: 0.7973 (pp30) cc_final: 0.7625 (pp30) REVERT: B 82 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 162 MET cc_start: 0.8683 (mmm) cc_final: 0.8243 (mmt) REVERT: B 206 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8631 (mt) REVERT: B 216 ILE cc_start: 0.9125 (tp) cc_final: 0.8862 (tt) REVERT: B 219 ILE cc_start: 0.7574 (mm) cc_final: 0.7198 (mm) REVERT: B 326 MET cc_start: 0.8716 (mmm) cc_final: 0.8356 (mmm) REVERT: C 38 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7867 (tm-30) REVERT: C 183 VAL cc_start: 0.7682 (OUTLIER) cc_final: 0.7436 (t) REVERT: C 218 LEU cc_start: 0.8064 (mp) cc_final: 0.7576 (tt) REVERT: C 276 LYS cc_start: 0.7611 (ttmt) cc_final: 0.6640 (tptt) REVERT: C 422 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7175 (mp0) REVERT: D 435 ASP cc_start: 0.7496 (m-30) cc_final: 0.7040 (t0) REVERT: E 38 GLN cc_start: 0.8798 (tm130) cc_final: 0.8350 (tt0) REVERT: E 82 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8453 (tp) REVERT: G 72 THR cc_start: 0.8146 (m) cc_final: 0.7902 (m) REVERT: G 95 THR cc_start: 0.8697 (m) cc_final: 0.8253 (p) REVERT: G 112 TRP cc_start: 0.7639 (t-100) cc_final: 0.6813 (t-100) REVERT: I 95 THR cc_start: 0.8815 (m) cc_final: 0.8529 (p) outliers start: 82 outliers final: 56 residues processed: 397 average time/residue: 0.1195 time to fit residues: 77.7114 Evaluate side-chains 388 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 328 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 92 LEU 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 79 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 206 ILE 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 79 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 183 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 49 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 215 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 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 97 TYR 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 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 47 THR 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 74 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 86 SER 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 145 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 217 optimal weight: 0.4980 chunk 175 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 ASN H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.151492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147192 restraints weight = 27100.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.146323 restraints weight = 30598.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144511 restraints weight = 34482.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.144306 restraints weight = 41461.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144099 restraints weight = 35009.910| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20626 Z= 0.117 Angle : 0.622 9.912 28235 Z= 0.296 Chirality : 0.043 0.283 3395 Planarity : 0.004 0.050 3319 Dihedral : 5.282 58.184 2666 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.31 % Allowed : 18.86 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2351 helix: 2.02 (0.20), residues: 733 sheet: -0.29 (0.22), residues: 586 loop : -1.68 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.015 0.001 TYR F 122 PHE 0.020 0.001 PHE B 412 TRP 0.012 0.001 TRP E 311 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (20571) covalent geometry : angle 0.60652 / 0.29 (28081) SS BOND : bond 0.00586 / 0.33 ( 11) SS BOND : angle 2.01945 / 1.45 ( 22) hydrogen bonds : bond 0.04316 / 2.81 ( 858) hydrogen bonds : angle 4.02934 / 2.75 ( 2703) link_ALPHA1-3 : bond 0.00907 / 0.51 ( 5) link_ALPHA1-3 : angle 1.56451 / 0.90 ( 15) link_ALPHA1-6 : bond 0.00566 / 0.31 ( 5) link_ALPHA1-6 : angle 1.32653 / 0.75 ( 15) link_BETA1-4 : bond 0.00459 / 0.28 ( 18) link_BETA1-4 : angle 1.44679 / 1.01 ( 54) link_NAG-ASN : bond 0.00515 / 0.29 ( 16) link_NAG-ASN : angle 2.61482 / 1.72 ( 48) *********************** 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 422 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 350 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7285 (mt-10) REVERT: A 14 ASP cc_start: 0.8291 (p0) cc_final: 0.7873 (p0) REVERT: A 37 MET cc_start: 0.8433 (tpp) cc_final: 0.8138 (ttt) REVERT: A 111 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8251 (mttm) REVERT: A 233 TYR cc_start: 0.7033 (t80) cc_final: 0.6710 (t80) REVERT: A 256 LEU cc_start: 0.8272 (tp) cc_final: 0.7986 (tp) REVERT: B 23 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8020 (mt) REVERT: B 38 GLN cc_start: 0.7953 (pp30) cc_final: 0.7551 (pp30) REVERT: B 82 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8490 (tp) REVERT: B 122 TRP cc_start: 0.8480 (t60) cc_final: 0.7023 (t60) REVERT: B 216 ILE cc_start: 0.9100 (tp) cc_final: 0.8859 (tt) REVERT: B 219 ILE cc_start: 0.7493 (mm) cc_final: 0.7089 (mm) REVERT: B 326 MET cc_start: 0.8459 (mmm) cc_final: 0.8089 (mmm) REVERT: B 446 MET cc_start: 0.7179 (tmm) cc_final: 0.5895 (ttt) REVERT: C 183 VAL cc_start: 0.7653 (OUTLIER) cc_final: 0.7370 (t) REVERT: C 218 LEU cc_start: 0.7917 (mp) cc_final: 0.7611 (tt) REVERT: C 276 LYS cc_start: 0.7550 (ttmt) cc_final: 0.6716 (tptt) REVERT: C 422 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6960 (mp0) REVERT: D 50 MET cc_start: 0.7962 (tmm) cc_final: 0.7727 (ttp) REVERT: E 38 GLN cc_start: 0.8726 (tm130) cc_final: 0.8359 (tt0) REVERT: E 82 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8478 (tp) REVERT: E 282 MET cc_start: 0.8150 (tpp) cc_final: 0.7862 (ttm) REVERT: E 435 MET cc_start: 0.7254 (ttp) cc_final: 0.6999 (ttm) REVERT: G 72 THR cc_start: 0.8020 (m) cc_final: 0.7703 (m) REVERT: G 95 THR cc_start: 0.8397 (m) cc_final: 0.8045 (p) REVERT: G 112 TRP cc_start: 0.7408 (t-100) cc_final: 0.6623 (t-100) REVERT: I 95 THR cc_start: 0.8746 (m) cc_final: 0.8526 (p) outliers start: 72 outliers final: 54 residues processed: 401 average time/residue: 0.1280 time to fit residues: 83.1071 Evaluate side-chains 388 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 148 SER 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 278 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 ILE 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 20 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 79 VAL 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 436 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 ASP 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 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 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 47 THR 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 122 TYR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 43 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 97 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.148857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138175 restraints weight = 27346.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.132067 restraints weight = 42954.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130923 restraints weight = 37571.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131147 restraints weight = 33755.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131279 restraints weight = 28466.040| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20626 Z= 0.155 Angle : 0.649 9.374 28235 Z= 0.311 Chirality : 0.044 0.275 3395 Planarity : 0.004 0.053 3319 Dihedral : 5.304 57.465 2666 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.05 % Allowed : 18.40 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2351 helix: 2.03 (0.20), residues: 733 sheet: -0.30 (0.21), residues: 594 loop : -1.64 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.015 0.001 TYR F 114 PHE 0.021 0.001 PHE B 412 TRP 0.012 0.001 TRP E 311 HIS 0.004 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (20571) covalent geometry : angle 0.63259 / 0.31 (28081) SS BOND : bond 0.00639 / 0.37 ( 11) SS BOND : angle 2.18832 / 1.57 ( 22) hydrogen bonds : bond 0.04467 / 2.91 ( 858) hydrogen bonds : angle 4.06196 / 2.77 ( 2703) link_ALPHA1-3 : bond 0.00923 / 0.50 ( 5) link_ALPHA1-3 : angle 1.58074 / 0.90 ( 15) link_ALPHA1-6 : bond 0.00562 / 0.30 ( 5) link_ALPHA1-6 : angle 1.29707 / 0.73 ( 15) link_BETA1-4 : bond 0.00452 / 0.29 ( 18) link_BETA1-4 : angle 1.50491 / 1.03 ( 54) link_NAG-ASN : bond 0.00346 / 0.23 ( 16) link_NAG-ASN : angle 2.78428 / 1.79 ( 48) *********************** 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 427 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 339 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8344 (p0) cc_final: 0.7930 (p0) REVERT: A 92 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6435 (tt) REVERT: A 233 TYR cc_start: 0.7155 (t80) cc_final: 0.6874 (t80) REVERT: B 23 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8195 (mt) REVERT: B 38 GLN cc_start: 0.8082 (pp30) cc_final: 0.7773 (pp30) REVERT: B 41 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9180 (tp) REVERT: B 82 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8514 (tp) REVERT: B 216 ILE cc_start: 0.9109 (tp) cc_final: 0.8877 (tt) REVERT: B 219 ILE cc_start: 0.7537 (mm) cc_final: 0.7141 (mm) REVERT: B 326 MET cc_start: 0.8732 (mmm) cc_final: 0.8420 (mmm) REVERT: C 183 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7423 (t) REVERT: C 218 LEU cc_start: 0.8073 (mp) cc_final: 0.7663 (tt) REVERT: C 276 LYS cc_start: 0.7663 (ttmt) cc_final: 0.6663 (tptt) REVERT: C 422 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7139 (mp0) REVERT: D 435 ASP cc_start: 0.7571 (m-30) cc_final: 0.7171 (t0) REVERT: E 38 GLN cc_start: 0.8794 (tm130) cc_final: 0.8423 (tt0) REVERT: E 82 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8554 (tp) REVERT: E 435 MET cc_start: 0.7422 (ttp) cc_final: 0.7111 (ttm) REVERT: F 22 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7290 (mm-40) REVERT: F 84 LYS cc_start: 0.8345 (tptp) cc_final: 0.7236 (pttp) REVERT: G 95 THR cc_start: 0.8802 (m) cc_final: 0.8372 (p) REVERT: G 112 TRP cc_start: 0.7623 (t-100) cc_final: 0.6813 (t-100) REVERT: I 95 THR cc_start: 0.8828 (m) cc_final: 0.8622 (p) outliers start: 88 outliers final: 67 residues processed: 400 average time/residue: 0.1254 time to fit residues: 82.1274 Evaluate side-chains 401 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 328 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 89 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR 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 23 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU 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 79 VAL 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 436 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 ASP 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 54 MET 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 110 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU 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 47 THR 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 G residue 44 THR Chi-restraints excluded: chain G residue 118 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 ASN H 24 GLN H 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.152286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.144497 restraints weight = 27203.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.140566 restraints weight = 33693.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.138861 restraints weight = 43271.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138994 restraints weight = 45177.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.139121 restraints weight = 35332.986| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20626 Z= 0.115 Angle : 0.626 12.063 28235 Z= 0.296 Chirality : 0.043 0.262 3395 Planarity : 0.004 0.051 3319 Dihedral : 5.153 57.755 2666 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.82 % Allowed : 19.04 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2351 helix: 2.16 (0.20), residues: 734 sheet: -0.17 (0.22), residues: 590 loop : -1.57 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.012 0.001 TYR F 114 PHE 0.023 0.001 PHE B 412 TRP 0.011 0.001 TRP E 311 HIS 0.005 0.001 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (20571) covalent geometry : angle 0.61048 / 0.29 (28081) SS BOND : bond 0.00556 / 0.30 ( 11) SS BOND : angle 1.88014 / 1.36 ( 22) hydrogen bonds : bond 0.04146 / 2.70 ( 858) hydrogen bonds : angle 3.91797 / 2.67 ( 2703) link_ALPHA1-3 : bond 0.00851 / 0.48 ( 5) link_ALPHA1-3 : angle 1.51309 / 0.87 ( 15) link_ALPHA1-6 : bond 0.00562 / 0.31 ( 5) link_ALPHA1-6 : angle 1.34218 / 0.75 ( 15) link_BETA1-4 : bond 0.00438 / 0.27 ( 18) link_BETA1-4 : angle 1.41476 / 0.99 ( 54) link_NAG-ASN : bond 0.00343 / 0.21 ( 16) link_NAG-ASN : angle 2.77256 / 1.75 ( 48) *********************** 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 417 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 334 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7431 (mt-10) REVERT: A 14 ASP cc_start: 0.8328 (p0) cc_final: 0.8017 (p0) REVERT: A 37 MET cc_start: 0.8504 (tpp) cc_final: 0.8203 (ttt) REVERT: A 92 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6387 (tt) REVERT: A 111 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8210 (mttm) REVERT: B 23 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8177 (mt) REVERT: B 38 GLN cc_start: 0.8051 (pp30) cc_final: 0.7675 (pp30) REVERT: B 41 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9166 (tp) REVERT: B 82 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8501 (tp) REVERT: B 122 TRP cc_start: 0.8474 (t60) cc_final: 0.6994 (t60) REVERT: B 216 ILE cc_start: 0.9057 (tp) cc_final: 0.8799 (tt) REVERT: B 219 ILE cc_start: 0.7515 (mm) cc_final: 0.7117 (mm) REVERT: B 326 MET cc_start: 0.8611 (mmm) cc_final: 0.8303 (mmm) REVERT: B 446 MET cc_start: 0.7267 (tmm) cc_final: 0.5939 (ttt) REVERT: C 183 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7351 (t) REVERT: C 218 LEU cc_start: 0.8012 (mp) cc_final: 0.7677 (tt) REVERT: C 276 LYS cc_start: 0.7566 (ttmt) cc_final: 0.6636 (tptt) REVERT: C 422 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7008 (mp0) REVERT: D 435 ASP cc_start: 0.7335 (m-30) cc_final: 0.6926 (t0) REVERT: E 38 GLN cc_start: 0.8746 (tm130) cc_final: 0.8430 (tt0) REVERT: E 82 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8538 (tp) REVERT: E 282 MET cc_start: 0.8235 (tpp) cc_final: 0.7984 (ttm) REVERT: E 435 MET cc_start: 0.7323 (ttp) cc_final: 0.7072 (ttm) REVERT: F 22 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7259 (mm-40) REVERT: G 95 THR cc_start: 0.8654 (m) cc_final: 0.8245 (p) REVERT: G 112 TRP cc_start: 0.7456 (t-100) cc_final: 0.6641 (t-100) REVERT: I 54 MET cc_start: 0.8032 (tmm) cc_final: 0.7790 (ptm) REVERT: I 95 THR cc_start: 0.8832 (m) cc_final: 0.8603 (p) outliers start: 83 outliers final: 60 residues processed: 391 average time/residue: 0.1280 time to fit residues: 81.3150 Evaluate side-chains 388 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 321 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 148 SER 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 278 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU 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 20 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 79 VAL 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 436 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 ASP 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 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 54 MET 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 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 47 THR 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 G residue 44 THR Chi-restraints excluded: chain G residue 118 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 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 73 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 115 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.151245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138913 restraints weight = 26908.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.137505 restraints weight = 43673.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138152 restraints weight = 41347.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138087 restraints weight = 28567.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.138317 restraints weight = 27562.717| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20626 Z= 0.122 Angle : 0.630 11.000 28235 Z= 0.300 Chirality : 0.043 0.259 3395 Planarity : 0.004 0.052 3319 Dihedral : 5.135 58.105 2666 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.59 % Allowed : 19.46 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.18), residues: 2351 helix: 2.30 (0.20), residues: 722 sheet: -0.22 (0.22), residues: 592 loop : -1.56 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 18 TYR 0.023 0.001 TYR A 233 PHE 0.024 0.001 PHE B 412 TRP 0.013 0.001 TRP B 430 HIS 0.002 0.001 HIS B 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (20571) covalent geometry : angle 0.61491 / 0.30 (28081) SS BOND : bond 0.00607 / 0.34 ( 11) SS BOND : angle 1.85168 / 1.32 ( 22) hydrogen bonds : bond 0.04124 / 2.68 ( 858) hydrogen bonds : angle 3.90758 / 2.66 ( 2703) link_ALPHA1-3 : bond 0.00894 / 0.49 ( 5) link_ALPHA1-3 : angle 1.51829 / 0.87 ( 15) link_ALPHA1-6 : bond 0.00579 / 0.31 ( 5) link_ALPHA1-6 : angle 1.33210 / 0.75 ( 15) link_BETA1-4 : bond 0.00443 / 0.28 ( 18) link_BETA1-4 : angle 1.42779 / 1.00 ( 54) link_NAG-ASN : bond 0.00383 / 0.25 ( 16) link_NAG-ASN : angle 2.60589 / 1.67 ( 48) *********************** 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 412 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 334 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7321 (mt-10) REVERT: A 14 ASP cc_start: 0.8344 (p0) cc_final: 0.8019 (p0) REVERT: A 37 MET cc_start: 0.8533 (tpp) cc_final: 0.8241 (ttt) REVERT: A 92 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6416 (tt) REVERT: A 233 TYR cc_start: 0.7120 (t80) cc_final: 0.6857 (t80) REVERT: B 23 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 38 GLN cc_start: 0.8075 (pp30) cc_final: 0.7680 (pp30) REVERT: B 41 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9168 (tp) REVERT: B 82 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8602 (tp) REVERT: B 122 TRP cc_start: 0.8489 (t60) cc_final: 0.7068 (t60) REVERT: B 216 ILE cc_start: 0.9005 (tp) cc_final: 0.8718 (tt) REVERT: B 219 ILE cc_start: 0.7504 (mm) cc_final: 0.7164 (mm) REVERT: B 326 MET cc_start: 0.8624 (mmm) cc_final: 0.8316 (mmm) REVERT: B 446 MET cc_start: 0.7329 (tmm) cc_final: 0.5973 (ttt) REVERT: C 183 VAL cc_start: 0.7660 (OUTLIER) cc_final: 0.7358 (t) REVERT: C 218 LEU cc_start: 0.8013 (mp) cc_final: 0.7640 (tt) REVERT: C 276 LYS cc_start: 0.7566 (ttmt) cc_final: 0.6533 (tptt) REVERT: C 422 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7027 (mp0) REVERT: D 435 ASP cc_start: 0.7420 (m-30) cc_final: 0.7004 (t0) REVERT: E 38 GLN cc_start: 0.8763 (tm130) cc_final: 0.8464 (tt0) REVERT: E 82 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8510 (tp) REVERT: E 282 MET cc_start: 0.8227 (tpp) cc_final: 0.7976 (ttm) REVERT: E 435 MET cc_start: 0.7305 (ttp) cc_final: 0.7075 (ttm) REVERT: F 22 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7272 (mm-40) REVERT: G 95 THR cc_start: 0.8751 (m) cc_final: 0.8346 (p) REVERT: G 112 TRP cc_start: 0.7467 (t-100) cc_final: 0.6641 (t-100) REVERT: I 95 THR cc_start: 0.8836 (m) cc_final: 0.8561 (p) REVERT: I 99 MET cc_start: 0.7079 (tpp) cc_final: 0.6203 (tpp) REVERT: I 115 ASN cc_start: 0.8147 (t0) cc_final: 0.7853 (m110) outliers start: 78 outliers final: 63 residues processed: 389 average time/residue: 0.1318 time to fit residues: 83.4311 Evaluate side-chains 395 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 326 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 148 SER 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 453 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 158 THR 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 79 VAL 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 436 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 ASP 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 54 MET 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 147 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 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 47 THR 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 G residue 44 THR Chi-restraints excluded: chain G residue 118 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 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 73 SER Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 29 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 136 optimal weight: 0.0170 chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145029 restraints weight = 26839.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140565 restraints weight = 34139.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138453 restraints weight = 38883.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.138437 restraints weight = 36280.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138507 restraints weight = 31058.744| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20626 Z= 0.114 Angle : 0.627 11.859 28235 Z= 0.297 Chirality : 0.043 0.254 3395 Planarity : 0.004 0.051 3319 Dihedral : 5.091 58.581 2666 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.13 % Allowed : 20.10 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.18), residues: 2351 helix: 2.35 (0.20), residues: 722 sheet: -0.18 (0.21), residues: 600 loop : -1.55 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.014 0.001 TYR C 76 PHE 0.025 0.001 PHE B 412 TRP 0.011 0.001 TRP E 311 HIS 0.003 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20571) covalent geometry : angle 0.61336 / 0.29 (28081) SS BOND : bond 0.00625 / 0.35 ( 11) SS BOND : angle 1.85428 / 1.34 ( 22) hydrogen bonds : bond 0.03991 / 2.60 ( 858) hydrogen bonds : angle 3.83905 / 2.61 ( 2703) link_ALPHA1-3 : bond 0.00818 / 0.45 ( 5) link_ALPHA1-3 : angle 1.48397 / 0.85 ( 15) link_ALPHA1-6 : bond 0.00577 / 0.32 ( 5) link_ALPHA1-6 : angle 1.34168 / 0.75 ( 15) link_BETA1-4 : bond 0.00442 / 0.28 ( 18) link_BETA1-4 : angle 1.41659 / 1.00 ( 54) link_NAG-ASN : bond 0.00352 / 0.22 ( 16) link_NAG-ASN : angle 2.49035 / 1.61 ( 48) ********************** 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 400 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 332 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7306 (mt-10) REVERT: A 14 ASP cc_start: 0.8268 (p0) cc_final: 0.7942 (p0) REVERT: A 37 MET cc_start: 0.8480 (tpp) cc_final: 0.8167 (ttt) REVERT: A 92 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6491 (tt) REVERT: A 148 SER cc_start: 0.9472 (OUTLIER) cc_final: 0.9205 (m) REVERT: A 233 TYR cc_start: 0.7130 (t80) cc_final: 0.6923 (t80) REVERT: B 23 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8186 (mt) REVERT: B 38 GLN cc_start: 0.8021 (pp30) cc_final: 0.7670 (pp30) REVERT: B 41 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9115 (tp) REVERT: B 82 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 122 TRP cc_start: 0.8433 (t60) cc_final: 0.7098 (t60) REVERT: B 216 ILE cc_start: 0.9006 (tp) cc_final: 0.8734 (tt) REVERT: B 219 ILE cc_start: 0.7567 (mm) cc_final: 0.7175 (mm) REVERT: B 251 LEU cc_start: 0.8098 (tt) cc_final: 0.7535 (mt) REVERT: B 326 MET cc_start: 0.8597 (mmm) cc_final: 0.8327 (mmm) REVERT: C 183 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7320 (t) REVERT: C 218 LEU cc_start: 0.7932 (mp) cc_final: 0.7630 (tt) REVERT: C 276 LYS cc_start: 0.7489 (ttmt) cc_final: 0.6570 (tptt) REVERT: C 422 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6975 (mp0) REVERT: D 91 VAL cc_start: 0.8623 (t) cc_final: 0.8374 (m) REVERT: D 435 ASP cc_start: 0.7319 (m-30) cc_final: 0.6913 (t0) REVERT: E 38 GLN cc_start: 0.8723 (tm130) cc_final: 0.8429 (tt0) REVERT: E 82 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8577 (tp) REVERT: E 282 MET cc_start: 0.8226 (tpp) cc_final: 0.7931 (ttm) REVERT: E 435 MET cc_start: 0.7297 (ttp) cc_final: 0.7080 (ttm) REVERT: F 22 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7204 (mm-40) REVERT: G 95 THR cc_start: 0.8712 (m) cc_final: 0.8310 (p) REVERT: G 112 TRP cc_start: 0.7447 (t-100) cc_final: 0.6639 (t-100) REVERT: H 79 TYR cc_start: 0.8338 (m-80) cc_final: 0.8111 (m-80) REVERT: I 95 THR cc_start: 0.8777 (m) cc_final: 0.8538 (p) REVERT: I 99 MET cc_start: 0.7112 (tpp) cc_final: 0.6139 (tpp) REVERT: I 100 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7385 (tp30) REVERT: I 115 ASN cc_start: 0.8143 (t0) cc_final: 0.7814 (m110) outliers start: 68 outliers final: 59 residues processed: 376 average time/residue: 0.1302 time to fit residues: 80.0218 Evaluate side-chains 389 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 323 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 148 SER 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 428 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU 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 271 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 157 ASP 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 4 ASN Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 54 MET 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 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 47 THR 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 G residue 44 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 122 TYR 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 73 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 14 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 212 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 118 optimal weight: 0.0470 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.144952 restraints weight = 26933.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137916 restraints weight = 43410.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.137120 restraints weight = 35680.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.136959 restraints weight = 40915.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.137303 restraints weight = 31207.605| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20626 Z= 0.108 Angle : 0.613 10.912 28235 Z= 0.292 Chirality : 0.042 0.252 3395 Planarity : 0.004 0.053 3319 Dihedral : 5.013 58.932 2666 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.17 % Allowed : 20.29 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2351 helix: 2.45 (0.20), residues: 721 sheet: -0.11 (0.22), residues: 600 loop : -1.48 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 75 TYR 0.021 0.001 TYR C 76 PHE 0.026 0.001 PHE B 412 TRP 0.011 0.001 TRP E 311 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (20571) covalent geometry : angle 0.59950 / 0.29 (28081) SS BOND : bond 0.00589 / 0.32 ( 11) SS BOND : angle 1.80961 / 1.30 ( 22) hydrogen bonds : bond 0.03843 / 2.50 ( 858) hydrogen bonds : angle 3.78904 / 2.58 ( 2703) link_ALPHA1-3 : bond 0.00797 / 0.44 ( 5) link_ALPHA1-3 : angle 1.46101 / 0.84 ( 15) link_ALPHA1-6 : bond 0.00568 / 0.31 ( 5) link_ALPHA1-6 : angle 1.34091 / 0.75 ( 15) link_BETA1-4 : bond 0.00433 / 0.27 ( 18) link_BETA1-4 : angle 1.39913 / 1.00 ( 54) link_NAG-ASN : bond 0.00355 / 0.22 ( 16) link_NAG-ASN : angle 2.35831 / 1.54 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3218.80 seconds wall clock time: 56 minutes 46.99 seconds (3406.99 seconds total)