Starting phenix.real_space_refine on Thu Mar 5 07:13:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pv8_20488/03_2026/6pv8_20488.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pv8_20488/03_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_20488/03_2026/6pv8_20488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pv8_20488/03_2026/6pv8_20488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pv8_20488/03_2026/6pv8_20488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pv8_20488/03_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-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'P1M': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'Y01:plan-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: 18 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: 18 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: 12 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: 18 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: 4.54, 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: 1.75 Conformation dependent library (CDL) restraints added in 812.3 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: 0.69 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: 3.64 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5951 1.36 - 1.50: 5903 1.50 - 1.64: 8509 1.64 - 1.78: 1 1.78 - 1.92: 207 Bond restraints: 20571 Sorted by residual: bond pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 1.332 1.583 -0.252 1.34e-02 5.57e+03 3.52e+02 bond pdb=" C3 P1M D 701 " pdb=" N8 P1M D 701 " ideal model delta sigma weight residual 1.457 1.530 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C3 P1M A 701 " pdb=" N8 P1M A 701 " ideal model delta sigma weight residual 1.457 1.529 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N ASN C 117 " pdb=" CA ASN C 117 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.18e-02 7.18e+03 1.23e+01 bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.96e+00 ... (remaining 20566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 27216 2.65 - 5.31: 716 5.31 - 7.96: 120 7.96 - 10.62: 18 10.62 - 13.27: 11 Bond angle restraints: 28081 Sorted by residual: angle pdb=" O LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 121.31 109.06 12.25 8.50e-01 1.38e+00 2.08e+02 angle pdb=" C LEU A 234 " pdb=" N PRO A 235 " pdb=" CA PRO A 235 " ideal model delta sigma weight residual 119.78 133.05 -13.27 1.03e+00 9.43e-01 1.66e+02 angle pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 119.19 130.10 -10.91 9.50e-01 1.11e+00 1.32e+02 angle pdb=" N TYR H 122 " pdb=" CA TYR H 122 " pdb=" C TYR H 122 " ideal model delta sigma weight residual 109.81 120.06 -10.25 2.21e+00 2.05e-01 2.15e+01 angle pdb=" N TYR F 122 " pdb=" CA TYR F 122 " pdb=" C TYR F 122 " ideal model delta sigma weight residual 109.81 120.01 -10.20 2.21e+00 2.05e-01 2.13e+01 ... (remaining 28076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 12858 27.68 - 55.35: 329 55.35 - 83.03: 59 83.03 - 110.70: 48 110.70 - 138.38: 3 Dihedral angle restraints: 13297 sinusoidal: 6243 harmonic: 7054 Sorted by residual: dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CB CYS D 128 " pdb=" SG CYS D 128 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual 93.00 48.72 44.28 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 13294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3207 0.133 - 0.265: 155 0.265 - 0.398: 23 0.398 - 0.530: 9 0.530 - 0.663: 1 Chirality restraints: 3395 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.52e+01 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 2.26 0.14 2.00e-02 2.50e+03 4.94e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.62e+01 ... (remaining 3392 not shown) Planarity restraints: 3335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " -0.269 2.00e-02 2.50e+03 2.26e-01 6.37e+02 pdb=" C7 NAG C 702 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " 0.381 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.187 2.00e-02 2.50e+03 1.55e-01 3.01e+02 pdb=" C7 NAG N 2 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.137 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.253 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 234 " 0.024 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C LEU A 234 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU A 234 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO A 235 " 0.022 2.00e-02 2.50e+03 ... (remaining 3332 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 141 2.63 - 3.19: 15928 3.19 - 3.76: 28623 3.76 - 4.33: 38330 4.33 - 4.90: 64291 Nonbonded interactions: 147313 Sorted by model distance: nonbonded pdb=" O GLY D 239 " pdb=" OE2 GLU E 241 " model vdw 2.057 3.040 nonbonded pdb=" O3 NAG C 702 " pdb=" O7 NAG C 702 " model vdw 2.109 3.040 nonbonded pdb=" NH1 ARG E 188 " pdb=" OD2 ASP E 204 " model vdw 2.113 3.120 nonbonded pdb=" OE2 GLU C 159 " pdb=" NH1 ARG D 79 " model vdw 2.237 3.120 nonbonded pdb=" OD1 ASP I 103 " pdb=" OH TYR I 107 " model vdw 2.306 3.040 ... (remaining 147308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 4 through 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.620 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.252 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 : 14.130 138.376 8694 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.69 % Allowed : 3.45 % Favored : 95.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00643 (20571) covalent geometry : angle 1.06742 (28081) SS BOND : bond 0.00792 ( 11) SS BOND : angle 1.60536 ( 22) hydrogen bonds : bond 0.16994 ( 858) hydrogen bonds : angle 6.27268 ( 2703) link_ALPHA1-3 : bond 0.00662 ( 5) link_ALPHA1-3 : angle 2.32867 ( 15) link_ALPHA1-6 : bond 0.00598 ( 5) link_ALPHA1-6 : angle 1.68350 ( 15) link_BETA1-4 : bond 0.00838 ( 18) link_BETA1-4 : angle 2.50988 ( 54) link_NAG-ASN : bond 0.01106 ( 16) link_NAG-ASN : angle 3.95768 ( 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 : 0.699 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: 0.1393 time to fit residues: 140.2488 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 : 0.671 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 166 ASN 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 F 78 ASN H 25 GLN H 81 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150943 restraints weight = 26332.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.147196 restraints weight = 40783.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145827 restraints weight = 39273.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.146197 restraints weight = 33309.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.146328 restraints weight = 27342.684| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20626 Z= 0.133 Angle : 0.699 9.946 28235 Z= 0.335 Chirality : 0.047 0.376 3395 Planarity : 0.005 0.050 3319 Dihedral : 13.074 131.054 4167 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.67 % Allowed : 12.56 % Favored : 84.77 % 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: -1.32 (0.16), residues: 2351 helix: 0.57 (0.19), residues: 734 sheet: -0.35 (0.21), residues: 583 loop : -2.31 (0.17), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 57 TYR 0.021 0.001 TYR F 122 PHE 0.018 0.001 PHE E 441 TRP 0.014 0.001 TRP C 122 HIS 0.012 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00281 (20571) covalent geometry : angle 0.67679 (28081) SS BOND : bond 0.00831 ( 11) SS BOND : angle 2.04938 ( 22) hydrogen bonds : bond 0.04861 ( 858) hydrogen bonds : angle 4.58877 ( 2703) link_ALPHA1-3 : bond 0.01504 ( 5) link_ALPHA1-3 : angle 1.94167 ( 15) link_ALPHA1-6 : bond 0.00867 ( 5) link_ALPHA1-6 : angle 1.98039 ( 15) link_BETA1-4 : bond 0.00606 ( 18) link_BETA1-4 : angle 2.22842 ( 54) link_NAG-ASN : bond 0.00542 ( 16) link_NAG-ASN : angle 3.02031 ( 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 479 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 421 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 SER cc_start: 0.9415 (t) cc_final: 0.9036 (m) REVERT: B 82 LEU cc_start: 0.8828 (tm) cc_final: 0.8513 (tp) REVERT: B 206 ILE cc_start: 0.8839 (pt) cc_final: 0.8595 (mt) REVERT: B 216 ILE cc_start: 0.9040 (tp) cc_final: 0.8750 (tt) REVERT: B 219 ILE cc_start: 0.7587 (mm) cc_final: 0.7280 (mm) REVERT: B 326 MET cc_start: 0.8630 (mmm) cc_final: 0.8224 (mmm) REVERT: B 446 MET cc_start: 0.7563 (tmm) cc_final: 0.5922 (ttt) REVERT: E 82 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8388 (tp) REVERT: F 110 SER cc_start: 0.7961 (m) cc_final: 0.7615 (t) REVERT: G 95 THR cc_start: 0.8442 (m) cc_final: 0.8068 (p) REVERT: G 112 TRP cc_start: 0.7106 (t-100) cc_final: 0.6112 (t-100) REVERT: H 117 SER cc_start: 0.9156 (p) cc_final: 0.8809 (m) REVERT: I 33 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7709 (ptm) REVERT: I 95 THR cc_start: 0.8699 (m) cc_final: 0.8207 (p) outliers start: 58 outliers final: 39 residues processed: 459 average time/residue: 0.1230 time to fit residues: 90.8568 Evaluate side-chains 384 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 343 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 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 95 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 33 MET Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 129 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN C 4 ASN C 192 ASN D 47 ASN H 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145721 restraints weight = 26849.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142330 restraints weight = 40640.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.140213 restraints weight = 37323.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140179 restraints weight = 36865.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.140427 restraints weight = 30449.475| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20626 Z= 0.170 Angle : 0.694 9.537 28235 Z= 0.333 Chirality : 0.047 0.372 3395 Planarity : 0.005 0.058 3319 Dihedral : 11.542 122.724 4158 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.91 % Allowed : 14.21 % Favored : 81.88 % 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: -0.79 (0.17), residues: 2351 helix: 1.32 (0.20), residues: 732 sheet: -0.30 (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 0.023 0.002 TYR F 128 PHE 0.021 0.002 PHE D 283 TRP 0.018 0.002 TRP E 311 HIS 0.004 0.001 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00395 (20571) covalent geometry : angle 0.67354 (28081) SS BOND : bond 0.00608 ( 11) SS BOND : angle 1.77405 ( 22) hydrogen bonds : bond 0.04798 ( 858) hydrogen bonds : angle 4.33872 ( 2703) link_ALPHA1-3 : bond 0.01614 ( 5) link_ALPHA1-3 : angle 1.50690 ( 15) link_ALPHA1-6 : bond 0.00849 ( 5) link_ALPHA1-6 : angle 2.03589 ( 15) link_BETA1-4 : bond 0.00548 ( 18) link_BETA1-4 : angle 2.08971 ( 54) link_NAG-ASN : bond 0.00489 ( 16) link_NAG-ASN : angle 3.09474 ( 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 450 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 365 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7774 (mttm) REVERT: B 82 LEU cc_start: 0.8883 (tm) cc_final: 0.8594 (tp) REVERT: B 206 ILE cc_start: 0.8853 (pt) cc_final: 0.8579 (mt) REVERT: B 216 ILE cc_start: 0.9048 (tp) cc_final: 0.8837 (tt) REVERT: B 219 ILE cc_start: 0.7645 (mm) cc_final: 0.7273 (mm) REVERT: B 326 MET cc_start: 0.8684 (mmm) cc_final: 0.8261 (mmm) REVERT: C 38 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7756 (tt0) REVERT: C 48 ASN cc_start: 0.8110 (t0) cc_final: 0.7408 (t0) REVERT: C 276 LYS cc_start: 0.7434 (ttmt) cc_final: 0.6595 (tptt) REVERT: D 435 ASP cc_start: 0.7282 (m-30) cc_final: 0.6840 (t0) REVERT: E 38 GLN cc_start: 0.8798 (tm130) cc_final: 0.8367 (tt0) REVERT: E 82 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8379 (tp) REVERT: G 95 THR cc_start: 0.8459 (m) cc_final: 0.8069 (p) REVERT: G 112 TRP cc_start: 0.7487 (t-100) cc_final: 0.6776 (t-100) REVERT: I 33 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7657 (ptm) REVERT: I 95 THR cc_start: 0.8784 (m) cc_final: 0.8367 (p) outliers start: 85 outliers final: 56 residues processed: 419 average time/residue: 0.1186 time to fit residues: 80.1346 Evaluate side-chains 396 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 337 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 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 156 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain 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 77 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 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: 6.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 217 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 198 optimal weight: 10.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS C 4 ASN D 317 ASN E 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.152275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143556 restraints weight = 26944.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.137339 restraints weight = 37922.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.135565 restraints weight = 36698.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.135603 restraints weight = 35570.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135928 restraints weight = 30966.097| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20626 Z= 0.158 Angle : 0.676 15.405 28235 Z= 0.321 Chirality : 0.046 0.356 3395 Planarity : 0.004 0.048 3319 Dihedral : 10.496 117.592 4158 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.96 % Allowed : 16.15 % Favored : 79.90 % 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: 1.67 (0.20), residues: 729 sheet: -0.29 (0.22), residues: 574 loop : -1.88 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.031 0.002 TYR E 234 PHE 0.019 0.001 PHE D 283 TRP 0.014 0.001 TRP E 311 HIS 0.004 0.001 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00367 (20571) covalent geometry : angle 0.65604 (28081) SS BOND : bond 0.00547 ( 11) SS BOND : angle 2.06671 ( 22) hydrogen bonds : bond 0.04617 ( 858) hydrogen bonds : angle 4.23846 ( 2703) link_ALPHA1-3 : bond 0.01529 ( 5) link_ALPHA1-3 : angle 1.63008 ( 15) link_ALPHA1-6 : bond 0.00847 ( 5) link_ALPHA1-6 : angle 1.90133 ( 15) link_BETA1-4 : bond 0.00559 ( 18) link_BETA1-4 : angle 1.99286 ( 54) link_NAG-ASN : bond 0.00417 ( 16) link_NAG-ASN : angle 2.97485 ( 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 442 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 356 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: 0.8124 (mm-30) cc_final: 0.7320 (mt-10) REVERT: A 37 MET cc_start: 0.8543 (tpp) cc_final: 0.8179 (ttt) REVERT: A 428 ASN cc_start: 0.7334 (t0) cc_final: 0.7063 (m-40) REVERT: B 82 LEU cc_start: 0.8829 (tm) cc_final: 0.8590 (tp) REVERT: B 162 MET cc_start: 0.8555 (mmm) cc_final: 0.8238 (mmt) REVERT: B 206 ILE cc_start: 0.8813 (pt) cc_final: 0.8608 (mt) REVERT: B 216 ILE cc_start: 0.9057 (tp) cc_final: 0.8832 (tt) REVERT: B 219 ILE cc_start: 0.7595 (mm) cc_final: 0.7198 (mm) REVERT: B 326 MET cc_start: 0.8731 (mmm) cc_final: 0.8327 (mmm) REVERT: B 446 MET cc_start: 0.7539 (tmm) cc_final: 0.6097 (ttt) REVERT: C 11 ASP cc_start: 0.7934 (m-30) cc_final: 0.7643 (m-30) REVERT: C 38 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7768 (tt0) REVERT: C 276 LYS cc_start: 0.7566 (ttmt) cc_final: 0.6619 (tptt) REVERT: D 191 ASN cc_start: 0.7315 (t0) cc_final: 0.6879 (t0) REVERT: D 325 MET cc_start: 0.6892 (mmt) cc_final: 0.6510 (mmt) REVERT: D 435 ASP cc_start: 0.7341 (m-30) cc_final: 0.6877 (t0) REVERT: E 38 GLN cc_start: 0.8802 (tm130) cc_final: 0.8455 (tt0) REVERT: E 82 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8406 (tp) REVERT: E 282 MET cc_start: 0.8157 (tpp) cc_final: 0.7869 (ttm) REVERT: F 22 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7220 (mm110) REVERT: G 95 THR cc_start: 0.8650 (m) cc_final: 0.8253 (p) REVERT: G 112 TRP cc_start: 0.7529 (t-100) cc_final: 0.6706 (t-100) REVERT: I 95 THR cc_start: 0.8791 (m) cc_final: 0.8455 (p) outliers start: 86 outliers final: 58 residues processed: 414 average time/residue: 0.1200 time to fit residues: 81.3199 Evaluate side-chains 393 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 334 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 264 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 215 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 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 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 86 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 208 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 210 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN D 298 HIS H 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.139230 restraints weight = 27272.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134561 restraints weight = 39585.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.132881 restraints weight = 42790.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.133404 restraints weight = 38772.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.133338 restraints weight = 30329.235| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20626 Z= 0.211 Angle : 0.736 10.615 28235 Z= 0.352 Chirality : 0.048 0.351 3395 Planarity : 0.005 0.054 3319 Dihedral : 10.202 114.879 4158 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.97 % Allowed : 16.42 % Favored : 78.61 % 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: -0.54 (0.17), residues: 2351 helix: 1.67 (0.20), residues: 730 sheet: -0.51 (0.21), residues: 596 loop : -1.81 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 82 TYR 0.027 0.002 TYR E 234 PHE 0.021 0.002 PHE D 283 TRP 0.014 0.002 TRP E 311 HIS 0.006 0.001 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00504 (20571) covalent geometry : angle 0.71710 (28081) SS BOND : bond 0.00656 ( 11) SS BOND : angle 2.28597 ( 22) hydrogen bonds : bond 0.05015 ( 858) hydrogen bonds : angle 4.34719 ( 2703) link_ALPHA1-3 : bond 0.01522 ( 5) link_ALPHA1-3 : angle 1.64725 ( 15) link_ALPHA1-6 : bond 0.00829 ( 5) link_ALPHA1-6 : angle 1.82231 ( 15) link_BETA1-4 : bond 0.00542 ( 18) link_BETA1-4 : angle 1.87662 ( 54) link_NAG-ASN : bond 0.00471 ( 16) link_NAG-ASN : angle 3.02901 ( 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 449 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 341 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7262 (mt-10) REVERT: A 14 ASP cc_start: 0.8378 (p0) cc_final: 0.7946 (p0) REVERT: A 92 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6387 (tt) REVERT: B 38 GLN cc_start: 0.8056 (pp30) cc_final: 0.7824 (tm-30) REVERT: B 41 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9242 (tp) REVERT: B 82 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8647 (tp) REVERT: B 162 MET cc_start: 0.8654 (mmm) cc_final: 0.8329 (mmt) REVERT: B 206 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8640 (mt) REVERT: B 216 ILE cc_start: 0.9158 (tp) cc_final: 0.8922 (tt) REVERT: B 219 ILE cc_start: 0.7635 (mm) cc_final: 0.7211 (mm) REVERT: B 326 MET cc_start: 0.8723 (mmm) cc_final: 0.8347 (mmm) REVERT: C 183 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7612 (t) REVERT: C 276 LYS cc_start: 0.7701 (ttmt) cc_final: 0.6790 (tptt) REVERT: C 422 GLU cc_start: 0.7645 (mt-10) cc_final: 0.6961 (mp0) REVERT: D 435 ASP cc_start: 0.7382 (m-30) cc_final: 0.6960 (t0) REVERT: E 38 GLN cc_start: 0.8894 (tm130) cc_final: 0.8456 (tt0) REVERT: E 133 LYS cc_start: 0.7539 (mmtt) cc_final: 0.7241 (pptt) REVERT: E 289 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8781 (tt) REVERT: G 95 THR cc_start: 0.8687 (m) cc_final: 0.8252 (p) REVERT: G 112 TRP cc_start: 0.7665 (t-100) cc_final: 0.6873 (t-100) REVERT: I 95 THR cc_start: 0.8795 (m) cc_final: 0.8531 (p) outliers start: 108 outliers final: 82 residues processed: 419 average time/residue: 0.1238 time to fit residues: 84.1192 Evaluate side-chains 410 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 322 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 115 GLU 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 447 ILE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 171 MET 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 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 91 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 215 ILE 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 306 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 322 VAL 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 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 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 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 97 THR 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 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 134 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 86 SER Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 145 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 175 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 HIS C 300 HIS E 416 HIS H 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142576 restraints weight = 26992.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.134926 restraints weight = 35812.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.134023 restraints weight = 34740.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134151 restraints weight = 33415.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134455 restraints weight = 27518.126| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20626 Z= 0.120 Angle : 0.643 9.559 28235 Z= 0.305 Chirality : 0.045 0.328 3395 Planarity : 0.004 0.046 3319 Dihedral : 9.700 111.158 4158 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.27 % Allowed : 18.68 % Favored : 78.06 % 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: -0.25 (0.18), residues: 2351 helix: 1.97 (0.20), residues: 735 sheet: -0.33 (0.21), residues: 584 loop : -1.70 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.028 0.001 TYR E 234 PHE 0.019 0.001 PHE B 412 TRP 0.011 0.001 TRP E 311 HIS 0.002 0.000 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00262 (20571) covalent geometry : angle 0.62421 (28081) SS BOND : bond 0.00602 ( 11) SS BOND : angle 1.97252 ( 22) hydrogen bonds : bond 0.04423 ( 858) hydrogen bonds : angle 4.11392 ( 2703) link_ALPHA1-3 : bond 0.01365 ( 5) link_ALPHA1-3 : angle 1.70927 ( 15) link_ALPHA1-6 : bond 0.00910 ( 5) link_ALPHA1-6 : angle 1.77356 ( 15) link_BETA1-4 : bond 0.00490 ( 18) link_BETA1-4 : angle 1.69777 ( 54) link_NAG-ASN : bond 0.00367 ( 16) link_NAG-ASN : angle 2.91330 ( 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 419 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 348 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8316 (p0) cc_final: 0.7970 (p0) REVERT: A 37 MET cc_start: 0.8517 (tpp) cc_final: 0.8213 (ttt) REVERT: B 82 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8512 (tp) REVERT: B 162 MET cc_start: 0.8633 (mmm) cc_final: 0.8211 (mmt) REVERT: B 216 ILE cc_start: 0.9078 (tp) cc_final: 0.8817 (tt) REVERT: B 219 ILE cc_start: 0.7543 (mm) cc_final: 0.7149 (mm) REVERT: B 326 MET cc_start: 0.8715 (mmm) cc_final: 0.8370 (mmm) REVERT: B 446 MET cc_start: 0.7366 (tmm) cc_final: 0.6055 (ttt) REVERT: C 276 LYS cc_start: 0.7572 (ttmt) cc_final: 0.6543 (tptt) REVERT: C 422 GLU cc_start: 0.7704 (mt-10) cc_final: 0.6918 (mp0) REVERT: D 191 ASN cc_start: 0.7641 (t0) cc_final: 0.7225 (t0) REVERT: E 38 GLN cc_start: 0.8770 (tm130) cc_final: 0.8490 (tt0) REVERT: E 82 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8511 (tp) REVERT: E 133 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7334 (pttt) REVERT: E 282 MET cc_start: 0.8189 (tpp) cc_final: 0.7926 (ttm) REVERT: F 84 LYS cc_start: 0.8246 (tptp) cc_final: 0.7210 (pttp) REVERT: G 95 THR cc_start: 0.8794 (m) cc_final: 0.8362 (p) REVERT: G 112 TRP cc_start: 0.7436 (t-100) cc_final: 0.6650 (t-100) REVERT: H 99 TYR cc_start: 0.8433 (m-80) cc_final: 0.8226 (m-80) REVERT: I 95 THR cc_start: 0.8789 (m) cc_final: 0.8523 (p) outliers start: 71 outliers final: 55 residues processed: 394 average time/residue: 0.1278 time to fit residues: 80.5791 Evaluate side-chains 385 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 328 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU 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 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 158 THR Chi-restraints excluded: chain C residue 222 CYS 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 215 ILE 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 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 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 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 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: 2.9990 chunk 187 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 0.0050 chunk 27 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142633 restraints weight = 26996.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142499 restraints weight = 37469.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142195 restraints weight = 35231.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 107)---------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135997 restraints weight = 34720.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.135572 restraints weight = 35279.671| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20626 Z= 0.123 Angle : 0.639 9.473 28235 Z= 0.302 Chirality : 0.045 0.334 3395 Planarity : 0.004 0.050 3319 Dihedral : 9.335 105.668 4158 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.54 % Allowed : 19.00 % Favored : 77.46 % 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: -0.10 (0.18), residues: 2351 helix: 2.08 (0.20), residues: 736 sheet: -0.20 (0.22), residues: 578 loop : -1.63 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.022 0.001 TYR C 76 PHE 0.021 0.001 PHE B 412 TRP 0.012 0.001 TRP E 311 HIS 0.010 0.001 HIS E 416 Details of bonding type rmsd covalent geometry : bond 0.00274 (20571) covalent geometry : angle 0.61939 (28081) SS BOND : bond 0.00578 ( 11) SS BOND : angle 1.97893 ( 22) hydrogen bonds : bond 0.04243 ( 858) hydrogen bonds : angle 4.01849 ( 2703) link_ALPHA1-3 : bond 0.01342 ( 5) link_ALPHA1-3 : angle 1.70959 ( 15) link_ALPHA1-6 : bond 0.00983 ( 5) link_ALPHA1-6 : angle 1.72281 ( 15) link_BETA1-4 : bond 0.00547 ( 18) link_BETA1-4 : angle 1.65755 ( 54) link_NAG-ASN : bond 0.00399 ( 16) link_NAG-ASN : angle 2.94905 ( 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 429 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 352 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8317 (p0) cc_final: 0.7923 (p0) REVERT: A 37 MET cc_start: 0.8530 (tpp) cc_final: 0.8197 (ttt) REVERT: A 233 TYR cc_start: 0.7285 (t80) cc_final: 0.6995 (t80) REVERT: B 41 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9217 (tp) REVERT: B 82 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8503 (tp) REVERT: B 122 TRP cc_start: 0.8449 (t60) cc_final: 0.6943 (t60) REVERT: B 216 ILE cc_start: 0.9038 (tp) cc_final: 0.8795 (tt) REVERT: B 219 ILE cc_start: 0.7504 (mm) cc_final: 0.7091 (mm) REVERT: B 326 MET cc_start: 0.8708 (mmm) cc_final: 0.8365 (mmm) REVERT: C 48 ASN cc_start: 0.8235 (t0) cc_final: 0.7203 (t0) REVERT: C 276 LYS cc_start: 0.7561 (ttmt) cc_final: 0.6684 (tptt) REVERT: C 422 GLU cc_start: 0.7614 (mt-10) cc_final: 0.6852 (mp0) REVERT: D 191 ASN cc_start: 0.7542 (t0) cc_final: 0.7177 (t0) REVERT: D 215 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8781 (mt) REVERT: D 435 ASP cc_start: 0.7438 (m-30) cc_final: 0.7045 (t0) REVERT: E 38 GLN cc_start: 0.8786 (tm130) cc_final: 0.8504 (tt0) REVERT: E 82 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8547 (tp) REVERT: E 133 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7307 (pttp) REVERT: E 282 MET cc_start: 0.8203 (tpp) cc_final: 0.7931 (ttm) REVERT: F 37 VAL cc_start: 0.7707 (m) cc_final: 0.7302 (p) REVERT: F 84 LYS cc_start: 0.8231 (tptp) cc_final: 0.7255 (pttp) REVERT: G 95 THR cc_start: 0.8729 (m) cc_final: 0.8323 (p) REVERT: G 112 TRP cc_start: 0.7416 (t-100) cc_final: 0.6648 (t-100) REVERT: I 95 THR cc_start: 0.8778 (m) cc_final: 0.8541 (p) REVERT: I 115 ASN cc_start: 0.8188 (t0) cc_final: 0.7971 (m110) outliers start: 77 outliers final: 57 residues processed: 403 average time/residue: 0.1188 time to fit residues: 77.8624 Evaluate side-chains 395 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 41 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU 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 171 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 35 ILE 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 158 THR 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 C residue 438 ASP Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 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 E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 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 59 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 117 SER 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 33 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.152300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142705 restraints weight = 27148.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142220 restraints weight = 46652.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.137939 restraints weight = 39726.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136315 restraints weight = 29750.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.136333 restraints weight = 31979.687| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20626 Z= 0.124 Angle : 0.641 12.083 28235 Z= 0.302 Chirality : 0.045 0.326 3395 Planarity : 0.004 0.049 3319 Dihedral : 9.073 103.258 4158 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.17 % Allowed : 19.64 % Favored : 77.18 % 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: -0.06 (0.18), residues: 2351 helix: 2.26 (0.20), residues: 724 sheet: -0.30 (0.21), residues: 599 loop : -1.61 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 75 TYR 0.021 0.001 TYR C 76 PHE 0.023 0.001 PHE B 412 TRP 0.012 0.001 TRP E 311 HIS 0.003 0.001 HIS E 416 Details of bonding type rmsd covalent geometry : bond 0.00278 (20571) covalent geometry : angle 0.62151 (28081) SS BOND : bond 0.00535 ( 11) SS BOND : angle 2.02965 ( 22) hydrogen bonds : bond 0.04164 ( 858) hydrogen bonds : angle 3.97212 ( 2703) link_ALPHA1-3 : bond 0.01245 ( 5) link_ALPHA1-3 : angle 1.70101 ( 15) link_ALPHA1-6 : bond 0.00999 ( 5) link_ALPHA1-6 : angle 1.67396 ( 15) link_BETA1-4 : bond 0.00507 ( 18) link_BETA1-4 : angle 1.61830 ( 54) link_NAG-ASN : bond 0.00480 ( 16) link_NAG-ASN : angle 2.97886 ( 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 411 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 342 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7410 (mt-10) REVERT: A 14 ASP cc_start: 0.8282 (p0) cc_final: 0.7968 (p0) REVERT: A 37 MET cc_start: 0.8500 (tpp) cc_final: 0.8174 (ttt) REVERT: A 111 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7924 (mttm) REVERT: A 233 TYR cc_start: 0.7237 (t80) cc_final: 0.6881 (t80) REVERT: B 41 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9195 (tp) REVERT: B 82 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8491 (tp) REVERT: B 122 TRP cc_start: 0.8478 (t60) cc_final: 0.6990 (t60) REVERT: B 216 ILE cc_start: 0.8973 (tp) cc_final: 0.8676 (tt) REVERT: B 219 ILE cc_start: 0.7495 (mm) cc_final: 0.7070 (mm) REVERT: B 313 LYS cc_start: 0.7444 (mttp) cc_final: 0.7199 (mttp) REVERT: B 326 MET cc_start: 0.8725 (mmm) cc_final: 0.8402 (mmm) REVERT: B 446 MET cc_start: 0.7369 (tmm) cc_final: 0.5975 (ttt) REVERT: C 276 LYS cc_start: 0.7558 (ttmt) cc_final: 0.6537 (tptt) REVERT: C 422 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6865 (mp0) REVERT: D 91 VAL cc_start: 0.8660 (t) cc_final: 0.8411 (m) REVERT: D 435 ASP cc_start: 0.7498 (m-30) cc_final: 0.7104 (t0) REVERT: E 38 GLN cc_start: 0.8791 (tm130) cc_final: 0.8445 (tt0) REVERT: E 82 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8506 (tp) REVERT: E 133 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7328 (pttp) REVERT: E 282 MET cc_start: 0.8215 (tpp) cc_final: 0.7948 (ttm) REVERT: G 95 THR cc_start: 0.8834 (m) cc_final: 0.8402 (p) REVERT: G 112 TRP cc_start: 0.7416 (t-100) cc_final: 0.6635 (t-100) REVERT: H 79 TYR cc_start: 0.8243 (m-80) cc_final: 0.7992 (m-80) REVERT: H 99 TYR cc_start: 0.8422 (m-80) cc_final: 0.8177 (m-80) REVERT: I 115 ASN cc_start: 0.8189 (t0) cc_final: 0.7929 (m110) outliers start: 69 outliers final: 55 residues processed: 387 average time/residue: 0.1243 time to fit residues: 78.4330 Evaluate side-chains 385 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 326 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU 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 171 MET Chi-restraints excluded: chain B residue 232 VAL 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 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 92 LEU Chi-restraints excluded: chain D residue 156 ILE 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 E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 115 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.0000 chunk 73 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN E 43 GLN 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 = 0.3662 r_free = 0.3662 target = 0.151240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142653 restraints weight = 26962.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.134841 restraints weight = 35885.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134669 restraints weight = 34139.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134707 restraints weight = 34760.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134817 restraints weight = 31207.115| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20626 Z= 0.132 Angle : 0.646 10.640 28235 Z= 0.307 Chirality : 0.045 0.342 3395 Planarity : 0.004 0.052 3319 Dihedral : 8.908 101.105 4158 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.22 % Allowed : 20.01 % 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: -0.02 (0.18), residues: 2351 helix: 2.30 (0.20), residues: 722 sheet: -0.24 (0.21), residues: 599 loop : -1.62 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 75 TYR 0.018 0.001 TYR C 76 PHE 0.025 0.001 PHE B 412 TRP 0.012 0.001 TRP E 311 HIS 0.003 0.001 HIS B 300 Details of bonding type rmsd covalent geometry : bond 0.00300 (20571) covalent geometry : angle 0.62781 (28081) SS BOND : bond 0.00606 ( 11) SS BOND : angle 1.96771 ( 22) hydrogen bonds : bond 0.04182 ( 858) hydrogen bonds : angle 3.95835 ( 2703) link_ALPHA1-3 : bond 0.01325 ( 5) link_ALPHA1-3 : angle 1.74933 ( 15) link_ALPHA1-6 : bond 0.01015 ( 5) link_ALPHA1-6 : angle 1.62154 ( 15) link_BETA1-4 : bond 0.00527 ( 18) link_BETA1-4 : angle 1.64326 ( 54) link_NAG-ASN : bond 0.00379 ( 16) link_NAG-ASN : angle 2.93242 ( 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 407 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 337 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7352 (mt-10) REVERT: A 14 ASP cc_start: 0.8295 (p0) cc_final: 0.7971 (p0) REVERT: A 37 MET cc_start: 0.8514 (tpp) cc_final: 0.8144 (ttt) REVERT: A 233 TYR cc_start: 0.7274 (t80) cc_final: 0.6912 (t80) REVERT: B 41 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9190 (tp) REVERT: B 82 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8521 (tp) REVERT: B 122 TRP cc_start: 0.8480 (t60) cc_final: 0.7102 (t60) REVERT: B 216 ILE cc_start: 0.8973 (tp) cc_final: 0.8725 (tt) REVERT: B 219 ILE cc_start: 0.7469 (mm) cc_final: 0.7120 (mm) REVERT: B 326 MET cc_start: 0.8727 (mmm) cc_final: 0.8457 (mmm) REVERT: C 183 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7541 (t) REVERT: C 276 LYS cc_start: 0.7527 (ttmt) cc_final: 0.6580 (tptt) REVERT: C 422 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6855 (mp0) REVERT: D 91 VAL cc_start: 0.8686 (t) cc_final: 0.8434 (m) REVERT: D 429 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7428 (tm-30) REVERT: D 435 ASP cc_start: 0.7552 (m-30) cc_final: 0.7179 (t0) REVERT: E 38 GLN cc_start: 0.8776 (tm130) cc_final: 0.8438 (tt0) REVERT: E 133 LYS cc_start: 0.7701 (mmtt) cc_final: 0.7275 (pttp) REVERT: E 234 TYR cc_start: 0.7891 (t80) cc_final: 0.7640 (t80) REVERT: E 282 MET cc_start: 0.8233 (tpp) cc_final: 0.7952 (ttm) REVERT: G 33 MET cc_start: 0.6953 (ppp) cc_final: 0.6661 (ppp) REVERT: G 95 THR cc_start: 0.8858 (m) cc_final: 0.8428 (p) REVERT: G 112 TRP cc_start: 0.7457 (t-100) cc_final: 0.6664 (t-100) REVERT: H 79 TYR cc_start: 0.8240 (m-80) cc_final: 0.7997 (m-80) REVERT: H 99 TYR cc_start: 0.8404 (m-80) cc_final: 0.8157 (m-80) REVERT: I 99 MET cc_start: 0.7239 (tpp) cc_final: 0.6382 (tpp) REVERT: I 115 ASN cc_start: 0.8165 (t0) cc_final: 0.7940 (m110) outliers start: 70 outliers final: 63 residues processed: 384 average time/residue: 0.1217 time to fit residues: 76.9306 Evaluate side-chains 396 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 330 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 260 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU 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 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 110 THR 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 92 LEU Chi-restraints excluded: chain D residue 156 ILE 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 E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 117 SER 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 52 THR 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 29 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145176 restraints weight = 26977.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139190 restraints weight = 38985.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138535 restraints weight = 34188.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138829 restraints weight = 27735.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.139228 restraints weight = 23082.537| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4238 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= 0.121 Angle : 0.638 10.878 28235 Z= 0.303 Chirality : 0.045 0.319 3395 Planarity : 0.004 0.050 3319 Dihedral : 8.702 98.393 4158 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.22 % Allowed : 20.10 % Favored : 76.68 % 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: 0.03 (0.18), residues: 2351 helix: 2.38 (0.20), residues: 721 sheet: -0.23 (0.21), residues: 603 loop : -1.61 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 321 TYR 0.019 0.001 TYR C 76 PHE 0.025 0.001 PHE B 412 TRP 0.011 0.001 TRP E 311 HIS 0.003 0.001 HIS I 55 Details of bonding type rmsd covalent geometry : bond 0.00272 (20571) covalent geometry : angle 0.61995 (28081) SS BOND : bond 0.00605 ( 11) SS BOND : angle 1.99493 ( 22) hydrogen bonds : bond 0.04047 ( 858) hydrogen bonds : angle 3.91275 ( 2703) link_ALPHA1-3 : bond 0.01193 ( 5) link_ALPHA1-3 : angle 1.70187 ( 15) link_ALPHA1-6 : bond 0.01044 ( 5) link_ALPHA1-6 : angle 1.55720 ( 15) link_BETA1-4 : bond 0.00509 ( 18) link_BETA1-4 : angle 1.60801 ( 54) link_NAG-ASN : bond 0.00375 ( 16) link_NAG-ASN : angle 2.81447 ( 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 406 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 336 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7357 (mt-10) REVERT: A 14 ASP cc_start: 0.8309 (p0) cc_final: 0.7975 (p0) REVERT: A 37 MET cc_start: 0.8494 (tpp) cc_final: 0.8181 (ttt) REVERT: A 111 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8284 (mttm) REVERT: A 233 TYR cc_start: 0.7235 (t80) cc_final: 0.6882 (t80) REVERT: B 41 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9138 (tp) REVERT: B 82 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8481 (tp) REVERT: B 122 TRP cc_start: 0.8456 (t60) cc_final: 0.7085 (t60) REVERT: B 216 ILE cc_start: 0.8966 (tp) cc_final: 0.8711 (tt) REVERT: B 219 ILE cc_start: 0.7594 (mm) cc_final: 0.7188 (mm) REVERT: B 251 LEU cc_start: 0.8121 (tt) cc_final: 0.7550 (mt) REVERT: B 326 MET cc_start: 0.8663 (mmm) cc_final: 0.8395 (mmm) REVERT: B 446 MET cc_start: 0.7400 (tmm) cc_final: 0.5987 (ttt) REVERT: C 183 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7477 (t) REVERT: C 276 LYS cc_start: 0.7481 (ttmt) cc_final: 0.6512 (tptt) REVERT: C 422 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6823 (mp0) REVERT: D 91 VAL cc_start: 0.8637 (t) cc_final: 0.8416 (m) REVERT: D 429 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7326 (tm-30) REVERT: D 435 ASP cc_start: 0.7437 (m-30) cc_final: 0.7053 (t0) REVERT: E 38 GLN cc_start: 0.8765 (tm130) cc_final: 0.8478 (tt0) REVERT: E 82 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8542 (tp) REVERT: E 133 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7304 (pttp) REVERT: E 234 TYR cc_start: 0.7909 (t80) cc_final: 0.7665 (t80) REVERT: E 282 MET cc_start: 0.8228 (tpp) cc_final: 0.7961 (ttm) REVERT: E 435 MET cc_start: 0.7395 (ttp) cc_final: 0.7127 (ttm) REVERT: F 22 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7261 (mm110) REVERT: G 95 THR cc_start: 0.8737 (m) cc_final: 0.8329 (p) REVERT: G 112 TRP cc_start: 0.7459 (t-100) cc_final: 0.6648 (t-100) REVERT: H 79 TYR cc_start: 0.8205 (m-80) cc_final: 0.7812 (m-80) REVERT: H 99 TYR cc_start: 0.8347 (m-80) cc_final: 0.8115 (m-80) REVERT: I 99 MET cc_start: 0.7135 (tpp) cc_final: 0.6263 (tpp) REVERT: I 115 ASN cc_start: 0.8174 (t0) cc_final: 0.7880 (m110) outliers start: 70 outliers final: 59 residues processed: 381 average time/residue: 0.1217 time to fit residues: 75.7301 Evaluate side-chains 395 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 171 MET 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 110 THR 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 C residue 438 ASP Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 156 ILE 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 E residue 23 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 304 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 117 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 14 optimal weight: 0.5980 chunk 182 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 64 optimal weight: 0.0370 chunk 197 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN H 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.153537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145046 restraints weight = 26907.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.138643 restraints weight = 37255.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137641 restraints weight = 36746.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.138137 restraints weight = 34208.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.138401 restraints weight = 27359.273| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20626 Z= 0.113 Angle : 0.626 10.964 28235 Z= 0.297 Chirality : 0.044 0.317 3395 Planarity : 0.004 0.052 3319 Dihedral : 8.452 94.332 4158 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.94 % Allowed : 20.15 % Favored : 76.91 % 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: 0.13 (0.18), residues: 2351 helix: 2.46 (0.20), residues: 721 sheet: -0.13 (0.21), residues: 598 loop : -1.57 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.019 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 E 416 Details of bonding type rmsd covalent geometry : bond 0.00247 (20571) covalent geometry : angle 0.60911 (28081) SS BOND : bond 0.00529 ( 11) SS BOND : angle 1.87090 ( 22) hydrogen bonds : bond 0.03861 ( 858) hydrogen bonds : angle 3.83299 ( 2703) link_ALPHA1-3 : bond 0.01177 ( 5) link_ALPHA1-3 : angle 1.67525 ( 15) link_ALPHA1-6 : bond 0.01036 ( 5) link_ALPHA1-6 : angle 1.47999 ( 15) link_BETA1-4 : bond 0.00514 ( 18) link_BETA1-4 : angle 1.59227 ( 54) link_NAG-ASN : bond 0.00370 ( 16) link_NAG-ASN : angle 2.70139 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.02 seconds wall clock time: 54 minutes 17.86 seconds (3257.86 seconds total)