Starting phenix.real_space_refine on Sun Sep 13 03:31:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.cif" model { file = "/net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pv7_20487/09_2026/6pv7_20487.cif" } resolution = 3.34 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= 0.004 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: 5 Type Number sf(0) Gaussians S 127 5.16 5 Na 1 4.78 5 C 13106 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 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20048 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "C" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3126 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {' NA': 1, 'NCT': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'DD9': 1, 'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'NCT': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 4.42, per 1000 atoms: 0.22 Number of scatterers: 20048 At special positions: 0 Unit cell: (151.94, 167.99, 157.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 127 16.00 Na 1 11.00 O 3720 8.00 N 3094 7.00 C 13106 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=2.04 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=2.05 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=2.03 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: 1.98 Conformation dependent library (CDL) restraints added in 837.5 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: 51 helices and 31 sheets defined 33.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.759A 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: 3.727A pdb=" N PHE A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 263 removed outlier: 3.657A pdb=" N LEU A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 removed outlier: 3.948A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.899A pdb=" N THR A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.794A pdb=" N VAL A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 463 removed outlier: 3.651A pdb=" N ALA A 441 " --> pdb=" O TRP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.584A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 14 " --> pdb=" O MET B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 5.575A 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: 3.885A pdb=" N LEU B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.675A 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: 4.102A pdb=" N GLU B 405 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.964A pdb=" N ARG C 75 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.538A pdb=" N ILE C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.588A 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 261 removed outlier: 3.905A pdb=" N LEU C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 298 removed outlier: 3.858A pdb=" N CYS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) 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: 4.266A pdb=" N GLU C 405 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 447 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.750A pdb=" N PHE D 12 " --> pdb=" O PHE D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.593A 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: 3.765A pdb=" N TYR D 233 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 263 removed outlier: 4.019A 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: 3.849A pdb=" N THR D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 removed outlier: 3.646A pdb=" N ARG D 321 " --> pdb=" O ASN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 464 removed outlier: 3.673A pdb=" N ALA D 441 " --> pdb=" O TRP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.574A pdb=" N LEU D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.595A pdb=" N LYS E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.692A pdb=" N ILE E 89 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 218 removed outlier: 3.568A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 230 removed outlier: 4.084A pdb=" N ILE E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 264 removed outlier: 3.984A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 298 removed outlier: 3.958A pdb=" N VAL E 298 " --> pdb=" O CYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 removed outlier: 3.728A pdb=" N PHE E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 324 removed outlier: 3.729A pdb=" N THR E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 457 removed outlier: 3.889A pdb=" N GLU E 405 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 407 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.611A pdb=" N ASP F 109 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.052A 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: 4.103A 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: 3.557A pdb=" N ASP H 109 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 4.160A 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: 4.142A 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: 3.885A 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: 3.885A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 42 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N TRP A 55 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N SER A 38 " --> pdb=" O TRP A 55 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A 57 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER A 36 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 59 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLU A 34 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ASN A 61 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N HIS A 32 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 146 removed outlier: 6.993A 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: 4.469A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.784A 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: 4.469A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 46 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN B 57 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU B 44 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TRP B 59 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA B 42 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS B 61 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER B 40 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLU B 63 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLN B 38 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR B 65 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 9.710A 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: 7.608A pdb=" N ILE B 206 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 183 " --> pdb=" O ILE B 206 " (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: 5.090A pdb=" N THR C 65 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER C 34 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE C 33 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL C 163 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.391A 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: 6.277A pdb=" N LEU C 44 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASN C 57 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.663A 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: 7.172A 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 109 through 110 Processing sheet with id=AB5, first strand: chain 'D' and resid 109 through 110 removed outlier: 3.605A pdb=" N LYS D 42 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN D 53 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 40 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N TRP D 55 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N SER D 38 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LYS D 57 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N SER D 36 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE D 59 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLU D 34 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 139 through 147 removed outlier: 7.183A 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 Processing sheet with id=AB9, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.649A pdb=" N SER E 46 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN E 57 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU E 44 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N TRP E 59 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA E 42 " --> pdb=" O TRP E 59 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS E 61 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER E 40 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU E 63 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLN E 38 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N THR E 65 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LYS E 36 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE E 33 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL E 163 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.523A 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: 5.478A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL E 199 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.634A 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: 5.478A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.658A 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: 3.613A pdb=" N THR F 136 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU F 53 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 69 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.662A 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 removed outlier: 3.613A pdb=" N THR F 136 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 27 through 29 removed outlier: 6.323A pdb=" N THR G 90 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N SER G 49 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N SER G 88 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 11.965A pdb=" N MET G 51 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N SER G 86 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 32 through 34 removed outlier: 3.543A pdb=" N MET G 33 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU G 126 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN G 58 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 5.693A 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: 6.601A pdb=" N LEU H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL H 69 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.680A 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 removed outlier: 12.121A pdb=" N CYS I 45 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N THR I 95 " --> pdb=" O CYS I 45 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N ALA I 47 " --> pdb=" O SER I 93 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N SER I 93 " --> pdb=" O ALA I 47 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N SER I 49 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER I 91 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.127A pdb=" N GLN I 58 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 5.726A 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: 3.543A pdb=" N THR I 118 " --> pdb=" O GLN I 111 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2625 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: 3.80 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5789 1.34 - 1.47: 5288 1.47 - 1.59: 9282 1.59 - 1.72: 0 1.72 - 1.84: 206 Bond restraints: 20565 Sorted by residual: bond pdb=" C LYS D 241 " pdb=" N VAL D 242 " ideal model delta sigma weight residual 1.335 1.473 -0.138 1.20e-02 6.94e+03 1.33e+02 bond pdb=" C LEU D 234 " pdb=" N PRO D 235 " ideal model delta sigma weight residual 1.329 1.415 -0.085 1.25e-02 6.40e+03 4.67e+01 bond pdb=" C TRP B 153 " pdb=" N THR B 154 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" C TRP C 153 " pdb=" N THR C 154 " ideal model delta sigma weight residual 1.334 1.381 -0.047 1.33e-02 5.65e+03 1.25e+01 bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 1.01e+01 ... (remaining 20560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 27178 2.77 - 5.53: 732 5.53 - 8.30: 118 8.30 - 11.07: 28 11.07 - 13.83: 10 Bond angle restraints: 28066 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 121.31 113.11 8.20 8.50e-01 1.38e+00 9.31e+01 angle pdb=" C LEU A 234 " pdb=" N PRO A 235 " pdb=" CA PRO A 235 " ideal model delta sigma weight residual 119.78 128.66 -8.88 1.03e+00 9.43e-01 7.44e+01 angle pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 119.19 126.76 -7.57 9.50e-01 1.11e+00 6.35e+01 angle pdb=" C LYS D 241 " pdb=" N VAL D 242 " pdb=" CA VAL D 242 " ideal model delta sigma weight residual 120.30 132.14 -11.84 1.64e+00 3.72e-01 5.21e+01 angle pdb=" O LYS D 241 " pdb=" C LYS D 241 " pdb=" N VAL D 242 " ideal model delta sigma weight residual 122.28 113.76 8.52 1.47e+00 4.63e-01 3.36e+01 ... (remaining 28061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.37: 11026 14.37 - 28.74: 582 28.74 - 43.11: 174 43.11 - 57.48: 23 57.48 - 71.85: 8 Dihedral angle restraints: 11813 sinusoidal: 4759 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 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+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 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+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 48.14 44.86 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 11810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3217 0.134 - 0.269: 143 0.269 - 0.403: 25 0.403 - 0.537: 5 0.537 - 0.672: 1 Chirality restraints: 3391 Sorted by residual: chirality pdb=" C1 MAN M 5 " pdb=" O6 BMA M 3 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.61e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.54e+01 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 7.02e+01 ... (remaining 3388 not shown) Planarity restraints: 3335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.118 2.00e-02 2.50e+03 9.73e-02 1.18e+02 pdb=" C7 NAG N 1 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.155 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.042 2.00e-02 2.50e+03 3.44e-02 1.48e+01 pdb=" C7 NAG N 2 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.054 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 152 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C SER E 152 " -0.053 2.00e-02 2.50e+03 pdb=" O SER E 152 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP E 153 " 0.018 2.00e-02 2.50e+03 ... (remaining 3332 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 62 2.54 - 3.13: 14032 3.13 - 3.72: 28641 3.72 - 4.31: 39984 4.31 - 4.90: 67428 Nonbonded interactions: 150147 Sorted by model distance: nonbonded pdb=" O GLY A 239 " pdb=" OE2 GLU B 241 " model vdw 1.952 3.040 nonbonded pdb=" O GLY D 239 " pdb=" OE2 GLU E 241 " model vdw 2.100 3.040 nonbonded pdb=" NH1 ARG E 188 " pdb=" OD2 ASP E 204 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASP C 181 " pdb=" NZ LYS C 210 " model vdw 2.297 3.120 nonbonded pdb=" O VAL A 22 " pdb=" ND2 ASN B 4 " model vdw 2.344 3.120 ... (remaining 150142 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' and resid 1 through 710) selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 4 through 712) selection = (chain 'C' and resid 4 through 712) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.900 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.007 0.138 20620 Z= 0.341 Angle : 1.139 13.833 28220 Z= 0.559 Chirality : 0.071 0.672 3391 Planarity : 0.008 0.097 3319 Dihedral : 10.046 71.855 7210 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.64 % Allowed : 3.54 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.91 (0.15), residues: 2351 helix: -1.56 (0.15), residues: 715 sheet: -0.90 (0.20), residues: 588 loop : -2.79 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 6 TYR 0.034 0.003 TYR B 97 PHE 0.037 0.003 PHE D 146 TRP 0.038 0.003 TRP E 122 HIS 0.006 0.002 HIS B 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00706 / 0.34 (20565) covalent geometry : angle 1.11892 / 0.56 (28066) SS BOND : bond 0.01021 / 0.56 ( 11) SS BOND : angle 1.69756 / 1.10 ( 22) hydrogen bonds : bond 0.13826 / 8.84 ( 834) hydrogen bonds : angle 5.89494 / 4.08 ( 2625) link_ALPHA1-3 : bond 0.00665 / 0.39 ( 5) link_ALPHA1-3 : angle 2.04663 / 1.07 ( 15) link_ALPHA1-6 : bond 0.00608 / 0.32 ( 5) link_ALPHA1-6 : angle 1.74745 / 0.93 ( 15) link_BETA1-4 : bond 0.00788 / 0.46 ( 18) link_BETA1-4 : angle 2.59290 / 1.76 ( 54) link_NAG-ASN : bond 0.00588 / 0.35 ( 16) link_NAG-ASN : angle 4.38019 / 3.17 ( 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 647 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 633 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: C 227 LEU cc_start: 0.8584 (tt) cc_final: 0.8067 (mt) REVERT: C 323 PHE cc_start: 0.8111 (t80) cc_final: 0.7860 (t80) REVERT: C 404 GLN cc_start: 0.7062 (tt0) cc_final: 0.6799 (mt0) REVERT: C 411 SER cc_start: 0.8287 (t) cc_final: 0.8082 (p) REVERT: D 92 LEU cc_start: 0.8056 (pt) cc_final: 0.7738 (tt) REVERT: D 172 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7294 (mm-30) REVERT: D 454 LEU cc_start: 0.7663 (tt) cc_final: 0.7164 (mt) REVERT: D 458 LEU cc_start: 0.7742 (tp) cc_final: 0.7467 (mm) REVERT: H 32 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6934 (mmp-170) REVERT: H 112 ILE cc_start: 0.8786 (mm) cc_final: 0.8553 (mt) REVERT: H 120 ASP cc_start: 0.7385 (p0) cc_final: 0.7076 (p0) outliers start: 14 outliers final: 3 residues processed: 644 average time/residue: 0.1422 time to fit residues: 140.8961 Evaluate side-chains 357 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 354 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain D residue 43 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.0170 overall best weight: 0.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 ASN B 144 GLN B 416 HIS D 48 GLN D 191 ASN D 428 ASN F 58 GLN F 81 GLN G 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.136249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112828 restraints weight = 27481.746| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.90 r_work: 0.3125 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20620 Z= 0.125 Angle : 0.678 14.347 28220 Z= 0.323 Chirality : 0.044 0.395 3391 Planarity : 0.005 0.043 3319 Dihedral : 6.047 60.631 2679 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.85 % Allowed : 11.64 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.28 (0.17), residues: 2351 helix: 0.64 (0.19), residues: 732 sheet: -0.38 (0.21), residues: 598 loop : -2.29 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 314 TYR 0.024 0.001 TYR F 122 PHE 0.025 0.001 PHE E 323 TRP 0.017 0.001 TRP D 118 HIS 0.003 0.001 HIS B 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20565) covalent geometry : angle 0.65238 / 0.32 (28066) SS BOND : bond 0.00596 / 0.30 ( 11) SS BOND : angle 1.09651 / 0.60 ( 22) hydrogen bonds : bond 0.05410 / 3.55 ( 834) hydrogen bonds : angle 4.47642 / 3.08 ( 2625) link_ALPHA1-3 : bond 0.01058 / 0.59 ( 5) link_ALPHA1-3 : angle 1.91327 / 1.04 ( 15) link_ALPHA1-6 : bond 0.00972 / 0.51 ( 5) link_ALPHA1-6 : angle 1.30234 / 0.74 ( 15) link_BETA1-4 : bond 0.00663 / 0.47 ( 18) link_BETA1-4 : angle 1.84762 / 1.32 ( 54) link_NAG-ASN : bond 0.00478 / 0.27 ( 16) link_NAG-ASN : angle 3.93093 / 2.70 ( 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 444 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 382 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 169 ASP cc_start: 0.7758 (t0) cc_final: 0.7519 (t0) REVERT: A 321 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7356 (ttm110) REVERT: B 31 GLN cc_start: 0.7596 (tt0) cc_final: 0.7127 (tt0) REVERT: B 79 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8666 (m) REVERT: B 230 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8110 (mm) REVERT: B 295 VAL cc_start: 0.8572 (p) cc_final: 0.8350 (m) REVERT: B 428 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: B 438 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: C 227 LEU cc_start: 0.8828 (tt) cc_final: 0.8212 (mt) REVERT: C 270 ASP cc_start: 0.7824 (t0) cc_final: 0.7588 (t0) REVERT: C 323 PHE cc_start: 0.8331 (t80) cc_final: 0.7851 (t80) REVERT: C 404 GLN cc_start: 0.7123 (tt0) cc_final: 0.6891 (mt0) REVERT: C 411 SER cc_start: 0.8291 (t) cc_final: 0.8081 (p) REVERT: C 422 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7722 (mp0) REVERT: C 435 MET cc_start: 0.8944 (ttm) cc_final: 0.8684 (ttm) REVERT: C 438 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: D 92 LEU cc_start: 0.8177 (pt) cc_final: 0.7521 (tt) REVERT: D 144 MET cc_start: 0.8697 (mtt) cc_final: 0.8425 (mtt) REVERT: D 323 MET cc_start: 0.8152 (mtm) cc_final: 0.7499 (mtm) REVERT: D 454 LEU cc_start: 0.7790 (tt) cc_final: 0.7116 (mt) REVERT: D 458 LEU cc_start: 0.7544 (tp) cc_final: 0.7104 (mm) REVERT: E 38 GLN cc_start: 0.8762 (tp40) cc_final: 0.8531 (tp40) REVERT: E 241 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7458 (mp0) REVERT: E 457 PHE cc_start: 0.5227 (m-10) cc_final: 0.4985 (m-10) REVERT: F 101 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7582 (mm-30) REVERT: G 74 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8500 (mm-40) REVERT: G 99 MET cc_start: 0.7879 (tpt) cc_final: 0.7627 (tpp) REVERT: H 32 ARG cc_start: 0.7370 (mtt180) cc_final: 0.6655 (mmp-170) REVERT: H 89 MET cc_start: 0.8995 (mtm) cc_final: 0.8680 (mtm) REVERT: H 120 ASP cc_start: 0.7741 (p0) cc_final: 0.7490 (p0) REVERT: I 63 THR cc_start: 0.8293 (t) cc_final: 0.8071 (m) REVERT: I 115 ASN cc_start: 0.8898 (m-40) cc_final: 0.8688 (m-40) outliers start: 62 outliers final: 36 residues processed: 423 average time/residue: 0.1280 time to fit residues: 86.4378 Evaluate side-chains 365 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 324 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain I residue 112 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 39 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 416 HIS D 48 GLN E 419 ASN F 58 GLN F 78 ASN G 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108314 restraints weight = 27646.544| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.98 r_work: 0.3023 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20620 Z= 0.161 Angle : 0.674 12.398 28220 Z= 0.319 Chirality : 0.044 0.349 3391 Planarity : 0.005 0.047 3319 Dihedral : 5.604 63.028 2672 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.05 % Allowed : 12.47 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.49 (0.18), residues: 2351 helix: 1.60 (0.20), residues: 727 sheet: -0.09 (0.22), residues: 594 loop : -1.95 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 6 TYR 0.017 0.002 TYR H 122 PHE 0.028 0.002 PHE E 323 TRP 0.015 0.001 TRP C 153 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (20565) covalent geometry : angle 0.65541 / 0.31 (28066) SS BOND : bond 0.00601 / 0.32 ( 11) SS BOND : angle 1.21905 / 0.69 ( 22) hydrogen bonds : bond 0.05199 / 3.39 ( 834) hydrogen bonds : angle 4.15967 / 2.86 ( 2625) link_ALPHA1-3 : bond 0.01004 / 0.54 ( 5) link_ALPHA1-3 : angle 1.64365 / 0.90 ( 15) link_ALPHA1-6 : bond 0.00714 / 0.37 ( 5) link_ALPHA1-6 : angle 1.32581 / 0.75 ( 15) link_BETA1-4 : bond 0.00577 / 0.38 ( 18) link_BETA1-4 : angle 1.81891 / 1.24 ( 54) link_NAG-ASN : bond 0.00499 / 0.30 ( 16) link_NAG-ASN : angle 3.22071 / 2.24 ( 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 426 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 338 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7855 (tt) REVERT: A 169 ASP cc_start: 0.7987 (t0) cc_final: 0.7702 (t0) REVERT: A 175 GLU cc_start: 0.8312 (tt0) cc_final: 0.8076 (tt0) REVERT: A 325 MET cc_start: 0.7254 (mtp) cc_final: 0.7030 (mtm) REVERT: A 445 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: B 31 GLN cc_start: 0.7731 (tt0) cc_final: 0.7232 (tt0) REVERT: B 79 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8694 (m) REVERT: B 207 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8620 (mt) REVERT: B 230 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 326 MET cc_start: 0.8044 (mmm) cc_final: 0.7785 (mtp) REVERT: B 428 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: B 438 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: C 75 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8146 (ttp-110) REVERT: C 192 ASN cc_start: 0.7690 (t0) cc_final: 0.7445 (p0) REVERT: C 227 LEU cc_start: 0.8910 (tt) cc_final: 0.8230 (mt) REVERT: C 270 ASP cc_start: 0.7833 (t0) cc_final: 0.7605 (t0) REVERT: C 404 GLN cc_start: 0.7042 (tt0) cc_final: 0.6799 (mt0) REVERT: C 422 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7779 (mp0) REVERT: D 92 LEU cc_start: 0.8350 (pt) cc_final: 0.7921 (tt) REVERT: D 291 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8742 (p) REVERT: D 428 ASN cc_start: 0.8150 (t0) cc_final: 0.7845 (m-40) REVERT: D 454 LEU cc_start: 0.7818 (tt) cc_final: 0.7044 (mt) REVERT: D 458 LEU cc_start: 0.7397 (tp) cc_final: 0.7081 (mm) REVERT: E 241 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8105 (mp0) REVERT: E 419 ASN cc_start: 0.8301 (m-40) cc_final: 0.7711 (m110) REVERT: E 457 PHE cc_start: 0.5255 (m-10) cc_final: 0.5002 (m-10) REVERT: F 101 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7688 (mm-30) REVERT: G 99 MET cc_start: 0.7934 (tpt) cc_final: 0.7627 (tpp) REVERT: H 32 ARG cc_start: 0.7420 (mtt180) cc_final: 0.6700 (mmp-170) outliers start: 88 outliers final: 54 residues processed: 398 average time/residue: 0.1273 time to fit residues: 81.1549 Evaluate side-chains 368 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 306 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain E residue 448 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 132 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 198 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN F 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106648 restraints weight = 27561.604| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.97 r_work: 0.3018 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20620 Z= 0.165 Angle : 0.646 9.437 28220 Z= 0.309 Chirality : 0.044 0.338 3391 Planarity : 0.004 0.045 3319 Dihedral : 5.465 64.334 2672 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.32 % Allowed : 14.54 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2351 helix: 1.87 (0.20), residues: 739 sheet: 0.05 (0.22), residues: 594 loop : -1.79 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 314 TYR 0.020 0.002 TYR E 128 PHE 0.029 0.002 PHE E 323 TRP 0.013 0.001 TRP B 153 HIS 0.004 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (20565) covalent geometry : angle 0.63011 / 0.30 (28066) SS BOND : bond 0.00556 / 0.29 ( 11) SS BOND : angle 1.20331 / 0.68 ( 22) hydrogen bonds : bond 0.05142 / 3.35 ( 834) hydrogen bonds : angle 4.02988 / 2.77 ( 2625) link_ALPHA1-3 : bond 0.00942 / 0.51 ( 5) link_ALPHA1-3 : angle 1.51067 / 0.83 ( 15) link_ALPHA1-6 : bond 0.00661 / 0.36 ( 5) link_ALPHA1-6 : angle 1.30290 / 0.73 ( 15) link_BETA1-4 : bond 0.00478 / 0.33 ( 18) link_BETA1-4 : angle 1.68630 / 1.18 ( 54) link_NAG-ASN : bond 0.00469 / 0.28 ( 16) link_NAG-ASN : angle 2.89684 / 2.02 ( 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 418 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 324 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8574 (ttt) cc_final: 0.8367 (ttt) REVERT: A 92 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 169 ASP cc_start: 0.7981 (t0) cc_final: 0.7687 (t0) REVERT: A 175 GLU cc_start: 0.8315 (tt0) cc_final: 0.8093 (tt0) REVERT: A 445 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8501 (m-30) REVERT: B 31 GLN cc_start: 0.7717 (tt0) cc_final: 0.7203 (tt0) REVERT: B 207 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 230 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 231 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.8960 (tp) REVERT: B 326 MET cc_start: 0.8062 (mmm) cc_final: 0.7778 (mtp) REVERT: B 428 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: B 438 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8294 (m-30) REVERT: C 75 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8333 (ttp-110) REVERT: C 227 LEU cc_start: 0.8931 (tt) cc_final: 0.8223 (mt) REVERT: C 270 ASP cc_start: 0.7859 (t0) cc_final: 0.7611 (t0) REVERT: C 404 GLN cc_start: 0.6984 (tt0) cc_final: 0.6727 (mt0) REVERT: C 411 SER cc_start: 0.8270 (t) cc_final: 0.8059 (p) REVERT: C 422 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7750 (mp0) REVERT: C 438 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: D 92 LEU cc_start: 0.8400 (pt) cc_final: 0.8006 (tt) REVERT: D 454 LEU cc_start: 0.7866 (tt) cc_final: 0.7183 (mt) REVERT: D 458 LEU cc_start: 0.7340 (tp) cc_final: 0.7097 (mm) REVERT: D 463 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8060 (tt) REVERT: E 50 ARG cc_start: 0.9031 (ttt90) cc_final: 0.8745 (mmm160) REVERT: E 179 GLU cc_start: 0.8055 (tp30) cc_final: 0.7755 (tp30) REVERT: E 241 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8105 (mp0) REVERT: E 457 PHE cc_start: 0.5262 (m-10) cc_final: 0.5058 (m-10) REVERT: F 82 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8864 (mtmt) REVERT: F 101 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7816 (mm-30) REVERT: G 74 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8720 (mm-40) REVERT: H 32 ARG cc_start: 0.7431 (mtt180) cc_final: 0.6635 (mmp-170) outliers start: 94 outliers final: 63 residues processed: 385 average time/residue: 0.1367 time to fit residues: 84.3888 Evaluate side-chains 378 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 306 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN D 48 GLN D 95 ASN E 4 ASN E 416 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.129362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.107341 restraints weight = 27490.256| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.77 r_work: 0.2971 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20620 Z= 0.133 Angle : 0.623 11.527 28220 Z= 0.295 Chirality : 0.043 0.326 3391 Planarity : 0.004 0.047 3319 Dihedral : 5.280 63.737 2672 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.19 % Allowed : 16.15 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.04 (0.18), residues: 2351 helix: 2.13 (0.20), residues: 739 sheet: 0.12 (0.22), residues: 594 loop : -1.69 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 314 TYR 0.016 0.001 TYR H 122 PHE 0.030 0.001 PHE E 323 TRP 0.011 0.001 TRP B 311 HIS 0.002 0.000 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (20565) covalent geometry : angle 0.60587 / 0.29 (28066) SS BOND : bond 0.00548 / 0.28 ( 11) SS BOND : angle 1.14124 / 0.62 ( 22) hydrogen bonds : bond 0.04873 / 3.18 ( 834) hydrogen bonds : angle 3.90045 / 2.67 ( 2625) link_ALPHA1-3 : bond 0.00996 / 0.53 ( 5) link_ALPHA1-3 : angle 1.45193 / 0.79 ( 15) link_ALPHA1-6 : bond 0.00619 / 0.34 ( 5) link_ALPHA1-6 : angle 1.30620 / 0.73 ( 15) link_BETA1-4 : bond 0.00491 / 0.33 ( 18) link_BETA1-4 : angle 1.59765 / 1.13 ( 54) link_NAG-ASN : bond 0.00385 / 0.22 ( 16) link_NAG-ASN : angle 2.96911 / 2.10 ( 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 418 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 327 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 169 ASP cc_start: 0.7946 (t0) cc_final: 0.7622 (t0) REVERT: A 175 GLU cc_start: 0.8214 (tt0) cc_final: 0.7990 (tt0) REVERT: A 445 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (m-30) REVERT: B 31 GLN cc_start: 0.7658 (tt0) cc_final: 0.7135 (tt0) REVERT: B 207 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8619 (mt) REVERT: B 227 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8218 (pp) REVERT: B 230 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8173 (mm) REVERT: B 326 MET cc_start: 0.8303 (mmm) cc_final: 0.7985 (mtp) REVERT: B 428 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: B 438 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: C 75 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8421 (ttp-110) REVERT: C 227 LEU cc_start: 0.8909 (tt) cc_final: 0.8199 (mt) REVERT: C 270 ASP cc_start: 0.7891 (t0) cc_final: 0.7672 (t0) REVERT: C 404 GLN cc_start: 0.6947 (tt0) cc_final: 0.6674 (mt0) REVERT: C 422 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7651 (mp0) REVERT: C 438 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: D 92 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7993 (tt) REVERT: D 291 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8652 (p) REVERT: D 454 LEU cc_start: 0.7729 (tt) cc_final: 0.7033 (mt) REVERT: D 458 LEU cc_start: 0.7278 (tp) cc_final: 0.7021 (mm) REVERT: D 463 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8072 (tt) REVERT: E 50 ARG cc_start: 0.8948 (ttt90) cc_final: 0.8713 (mmm160) REVERT: E 179 GLU cc_start: 0.7979 (tp30) cc_final: 0.7620 (tp30) REVERT: E 241 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8094 (mp0) REVERT: F 82 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8741 (mtmt) REVERT: F 101 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7633 (mm-30) REVERT: G 74 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8701 (mm-40) REVERT: H 32 ARG cc_start: 0.7367 (mtt180) cc_final: 0.6562 (mmp-170) REVERT: H 42 LYS cc_start: 0.8292 (tmmt) cc_final: 0.7706 (tptt) REVERT: H 82 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8406 (mtpp) outliers start: 91 outliers final: 63 residues processed: 381 average time/residue: 0.1340 time to fit residues: 81.4693 Evaluate side-chains 380 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 4 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 202 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 144 GLN D 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107440 restraints weight = 27499.073| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.77 r_work: 0.2972 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20620 Z= 0.130 Angle : 0.609 9.989 28220 Z= 0.290 Chirality : 0.043 0.324 3391 Planarity : 0.004 0.047 3319 Dihedral : 5.186 64.268 2672 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.05 % Allowed : 16.74 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.18), residues: 2351 helix: 2.27 (0.20), residues: 739 sheet: 0.10 (0.22), residues: 603 loop : -1.60 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 314 TYR 0.016 0.001 TYR H 122 PHE 0.030 0.001 PHE E 323 TRP 0.011 0.001 TRP B 311 HIS 0.002 0.000 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (20565) covalent geometry : angle 0.59224 / 0.29 (28066) SS BOND : bond 0.00546 / 0.28 ( 11) SS BOND : angle 1.13485 / 0.61 ( 22) hydrogen bonds : bond 0.04735 / 3.10 ( 834) hydrogen bonds : angle 3.79966 / 2.59 ( 2625) link_ALPHA1-3 : bond 0.00904 / 0.48 ( 5) link_ALPHA1-3 : angle 1.40912 / 0.77 ( 15) link_ALPHA1-6 : bond 0.00598 / 0.33 ( 5) link_ALPHA1-6 : angle 1.30253 / 0.73 ( 15) link_BETA1-4 : bond 0.00470 / 0.32 ( 18) link_BETA1-4 : angle 1.56107 / 1.10 ( 54) link_NAG-ASN : bond 0.00462 / 0.27 ( 16) link_NAG-ASN : angle 2.91964 / 2.08 ( 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 404 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 316 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7662 (pttm) REVERT: A 169 ASP cc_start: 0.8008 (t0) cc_final: 0.7671 (t0) REVERT: A 175 GLU cc_start: 0.8245 (tt0) cc_final: 0.8030 (tt0) REVERT: A 445 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8470 (m-30) REVERT: B 23 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8825 (mt) REVERT: B 31 GLN cc_start: 0.7636 (tt0) cc_final: 0.7148 (tt0) REVERT: B 230 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8231 (mm) REVERT: B 231 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8979 (tp) REVERT: B 326 MET cc_start: 0.8305 (mmm) cc_final: 0.7984 (mtp) REVERT: B 428 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: B 438 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8319 (m-30) REVERT: C 75 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8421 (ttp-110) REVERT: C 227 LEU cc_start: 0.8887 (tt) cc_final: 0.8170 (mt) REVERT: C 270 ASP cc_start: 0.7869 (t0) cc_final: 0.7666 (t0) REVERT: C 404 GLN cc_start: 0.7006 (tt0) cc_final: 0.6764 (mt0) REVERT: C 438 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7718 (m-30) REVERT: D 92 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8016 (tt) REVERT: D 291 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8697 (p) REVERT: D 454 LEU cc_start: 0.7844 (tt) cc_final: 0.7155 (mt) REVERT: D 458 LEU cc_start: 0.7272 (tp) cc_final: 0.6998 (mm) REVERT: D 463 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8116 (tt) REVERT: E 179 GLU cc_start: 0.8022 (tp30) cc_final: 0.7643 (tp30) REVERT: E 241 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8071 (mp0) REVERT: F 101 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7682 (mm-30) REVERT: G 74 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8714 (mm-40) REVERT: H 32 ARG cc_start: 0.7323 (mtt180) cc_final: 0.6544 (mmp-170) REVERT: H 82 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8419 (mtpp) outliers start: 88 outliers final: 67 residues processed: 369 average time/residue: 0.1391 time to fit residues: 82.0160 Evaluate side-chains 382 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 305 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN E 31 GLN E 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.105782 restraints weight = 27613.613| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.83 r_work: 0.2963 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 0.003 0.041 20620 Z= 0.132 Angle : 0.608 9.394 28220 Z= 0.290 Chirality : 0.043 0.321 3391 Planarity : 0.004 0.048 3319 Dihedral : 5.133 64.638 2672 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.14 % Allowed : 16.93 % Favored : 78.93 % 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: 0.24 (0.18), residues: 2351 helix: 2.36 (0.20), residues: 739 sheet: 0.10 (0.22), residues: 599 loop : -1.54 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 314 TYR 0.017 0.001 TYR D 419 PHE 0.032 0.001 PHE E 323 TRP 0.011 0.001 TRP B 311 HIS 0.003 0.000 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (20565) covalent geometry : angle 0.59227 / 0.29 (28066) SS BOND : bond 0.00531 / 0.28 ( 11) SS BOND : angle 1.11641 / 0.60 ( 22) hydrogen bonds : bond 0.04687 / 3.07 ( 834) hydrogen bonds : angle 3.74243 / 2.54 ( 2625) link_ALPHA1-3 : bond 0.00891 / 0.48 ( 5) link_ALPHA1-3 : angle 1.38525 / 0.76 ( 15) link_ALPHA1-6 : bond 0.00587 / 0.32 ( 5) link_ALPHA1-6 : angle 1.31119 / 0.73 ( 15) link_BETA1-4 : bond 0.00463 / 0.31 ( 18) link_BETA1-4 : angle 1.54764 / 1.09 ( 54) link_NAG-ASN : bond 0.00450 / 0.27 ( 16) link_NAG-ASN : angle 2.84890 / 2.04 ( 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 402 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 312 time to evaluate : 0.692 Fit side-chains REVERT: A 92 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 105 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7662 (pttm) REVERT: A 169 ASP cc_start: 0.8044 (t0) cc_final: 0.7709 (t0) REVERT: A 175 GLU cc_start: 0.8300 (tt0) cc_final: 0.8069 (tt0) REVERT: A 445 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: B 23 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8841 (mt) REVERT: B 31 GLN cc_start: 0.7617 (tt0) cc_final: 0.7113 (tt0) REVERT: B 230 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8285 (mm) REVERT: B 231 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8987 (tp) REVERT: B 326 MET cc_start: 0.8219 (mmm) cc_final: 0.7951 (mtp) REVERT: B 428 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: B 438 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: C 75 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8353 (ttp-110) REVERT: C 227 LEU cc_start: 0.8901 (tt) cc_final: 0.8169 (mt) REVERT: C 270 ASP cc_start: 0.7903 (t0) cc_final: 0.7694 (t0) REVERT: C 404 GLN cc_start: 0.6996 (tt0) cc_final: 0.6721 (mt0) REVERT: C 422 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7601 (mp0) REVERT: C 438 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: D 92 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8008 (tt) REVERT: D 291 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8657 (p) REVERT: D 454 LEU cc_start: 0.7799 (tt) cc_final: 0.7107 (mt) REVERT: D 458 LEU cc_start: 0.7155 (tp) cc_final: 0.6873 (mm) REVERT: D 463 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8046 (tt) REVERT: E 241 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8062 (mp0) REVERT: E 445 PHE cc_start: 0.6636 (m-10) cc_final: 0.6417 (m-10) REVERT: F 101 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7598 (mm-30) REVERT: G 74 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8748 (mm-40) REVERT: H 32 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6570 (mmp-170) REVERT: H 42 LYS cc_start: 0.8253 (tmmt) cc_final: 0.7581 (tptt) REVERT: H 82 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8484 (mtpp) outliers start: 90 outliers final: 69 residues processed: 364 average time/residue: 0.1285 time to fit residues: 75.0572 Evaluate side-chains 381 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 301 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 52 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 30 optimal weight: 0.0020 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 213 optimal weight: 0.0770 chunk 194 optimal weight: 3.9990 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100383 restraints weight = 28114.016| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.16 r_work: 0.2946 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20620 Z= 0.109 Angle : 0.580 9.398 28220 Z= 0.276 Chirality : 0.042 0.310 3391 Planarity : 0.004 0.049 3319 Dihedral : 4.967 62.165 2672 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.31 % Allowed : 18.22 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2351 helix: 2.51 (0.20), residues: 739 sheet: 0.21 (0.22), residues: 595 loop : -1.49 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 314 TYR 0.018 0.001 TYR D 419 PHE 0.030 0.001 PHE E 323 TRP 0.011 0.001 TRP A 60 HIS 0.001 0.000 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (20565) covalent geometry : angle 0.56421 / 0.27 (28066) SS BOND : bond 0.00536 / 0.27 ( 11) SS BOND : angle 1.09735 / 0.57 ( 22) hydrogen bonds : bond 0.04308 / 2.83 ( 834) hydrogen bonds : angle 3.61818 / 2.46 ( 2625) link_ALPHA1-3 : bond 0.00835 / 0.45 ( 5) link_ALPHA1-3 : angle 1.36816 / 0.75 ( 15) link_ALPHA1-6 : bond 0.00587 / 0.33 ( 5) link_ALPHA1-6 : angle 1.31388 / 0.74 ( 15) link_BETA1-4 : bond 0.00460 / 0.30 ( 18) link_BETA1-4 : angle 1.45674 / 1.04 ( 54) link_NAG-ASN : bond 0.00479 / 0.28 ( 16) link_NAG-ASN : angle 2.75698 / 1.97 ( 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 391 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 319 time to evaluate : 0.925 Fit side-chains REVERT: A 92 LEU cc_start: 0.8452 (pt) cc_final: 0.7745 (tt) REVERT: A 105 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7713 (pttm) REVERT: A 169 ASP cc_start: 0.8145 (t0) cc_final: 0.7820 (t0) REVERT: A 175 GLU cc_start: 0.8333 (tt0) cc_final: 0.8093 (tt0) REVERT: A 445 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: B 23 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8801 (mt) REVERT: B 31 GLN cc_start: 0.7637 (tt0) cc_final: 0.7075 (tt0) REVERT: B 51 GLU cc_start: 0.8504 (mp0) cc_final: 0.8251 (pm20) REVERT: B 79 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8552 (m) REVERT: B 227 LEU cc_start: 0.8382 (tt) cc_final: 0.7397 (mt) REVERT: B 230 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 231 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8960 (tp) REVERT: B 428 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: B 438 ASP cc_start: 0.8597 (t0) cc_final: 0.8365 (m-30) REVERT: C 75 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8258 (ttp-110) REVERT: C 227 LEU cc_start: 0.8907 (tt) cc_final: 0.8189 (mt) REVERT: C 270 ASP cc_start: 0.8026 (t0) cc_final: 0.7789 (t0) REVERT: C 404 GLN cc_start: 0.6899 (tt0) cc_final: 0.6598 (mt0) REVERT: C 422 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7515 (mp0) REVERT: D 291 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8490 (p) REVERT: D 454 LEU cc_start: 0.7608 (tt) cc_final: 0.6865 (mt) REVERT: D 458 LEU cc_start: 0.6912 (tp) cc_final: 0.6649 (mm) REVERT: E 241 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8230 (mp0) REVERT: E 445 PHE cc_start: 0.6518 (m-10) cc_final: 0.6291 (m-80) REVERT: F 101 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7429 (mm-30) REVERT: H 32 ARG cc_start: 0.7464 (mtt180) cc_final: 0.6490 (mmp-170) REVERT: H 42 LYS cc_start: 0.8119 (tmmt) cc_final: 0.7426 (tptt) REVERT: I 51 MET cc_start: 0.8318 (ptm) cc_final: 0.8094 (ptm) outliers start: 72 outliers final: 53 residues processed: 362 average time/residue: 0.1334 time to fit residues: 78.1101 Evaluate side-chains 369 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN E 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.099223 restraints weight = 28223.226| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.16 r_work: 0.3107 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20620 Z= 0.123 Angle : 0.602 9.393 28220 Z= 0.286 Chirality : 0.043 0.315 3391 Planarity : 0.004 0.054 3319 Dihedral : 4.937 59.856 2672 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.17 % Allowed : 18.63 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2351 helix: 2.54 (0.20), residues: 737 sheet: 0.17 (0.22), residues: 591 loop : -1.45 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 314 TYR 0.019 0.001 TYR D 419 PHE 0.033 0.001 PHE E 323 TRP 0.011 0.001 TRP F 66 HIS 0.002 0.000 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (20565) covalent geometry : angle 0.58639 / 0.28 (28066) SS BOND : bond 0.00531 / 0.27 ( 11) SS BOND : angle 1.10376 / 0.59 ( 22) hydrogen bonds : bond 0.04412 / 2.89 ( 834) hydrogen bonds : angle 3.63356 / 2.46 ( 2625) link_ALPHA1-3 : bond 0.00821 / 0.44 ( 5) link_ALPHA1-3 : angle 1.35022 / 0.74 ( 15) link_ALPHA1-6 : bond 0.00576 / 0.32 ( 5) link_ALPHA1-6 : angle 1.32285 / 0.74 ( 15) link_BETA1-4 : bond 0.00453 / 0.30 ( 18) link_BETA1-4 : angle 1.49664 / 1.06 ( 54) link_NAG-ASN : bond 0.00450 / 0.27 ( 16) link_NAG-ASN : angle 2.73446 / 1.96 ( 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 376 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 307 time to evaluate : 0.819 Fit side-chains REVERT: A 92 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7800 (tt) REVERT: A 105 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7726 (pttm) REVERT: A 169 ASP cc_start: 0.8181 (t0) cc_final: 0.7935 (t0) REVERT: A 175 GLU cc_start: 0.8346 (tt0) cc_final: 0.8135 (tt0) REVERT: B 23 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8795 (mt) REVERT: B 31 GLN cc_start: 0.7738 (tt0) cc_final: 0.7182 (tt0) REVERT: B 79 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8537 (m) REVERT: B 227 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7434 (mt) REVERT: B 230 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8295 (mm) REVERT: B 231 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8948 (tp) REVERT: B 428 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: B 438 ASP cc_start: 0.8616 (t0) cc_final: 0.8380 (m-30) REVERT: C 75 ARG cc_start: 0.8643 (ttm-80) cc_final: 0.8330 (ttp-110) REVERT: C 227 LEU cc_start: 0.8925 (tt) cc_final: 0.8190 (mt) REVERT: C 270 ASP cc_start: 0.7991 (t0) cc_final: 0.7769 (t0) REVERT: C 404 GLN cc_start: 0.6937 (tt0) cc_final: 0.6645 (mt0) REVERT: D 83 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8644 (mp10) REVERT: D 291 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8515 (p) REVERT: D 454 LEU cc_start: 0.7649 (tt) cc_final: 0.6930 (mt) REVERT: D 458 LEU cc_start: 0.7022 (tp) cc_final: 0.6729 (mm) REVERT: E 241 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8234 (mp0) REVERT: E 445 PHE cc_start: 0.6579 (m-10) cc_final: 0.6348 (m-80) REVERT: F 101 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7550 (mm-30) REVERT: G 112 TRP cc_start: 0.7058 (t-100) cc_final: 0.6257 (t-100) REVERT: H 32 ARG cc_start: 0.7512 (mtt180) cc_final: 0.6546 (mmp-170) REVERT: I 51 MET cc_start: 0.8403 (ptm) cc_final: 0.8163 (ptm) outliers start: 69 outliers final: 55 residues processed: 350 average time/residue: 0.1369 time to fit residues: 77.2895 Evaluate side-chains 364 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 181 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 97 optimal weight: 0.0670 chunk 204 optimal weight: 4.9990 chunk 152 optimal weight: 0.0040 chunk 68 optimal weight: 0.0770 chunk 88 optimal weight: 0.0070 chunk 185 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 164 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.0506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 194 GLN D 48 GLN E 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.104377 restraints weight = 28125.872| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.19 r_work: 0.3185 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20620 Z= 0.099 Angle : 0.560 9.386 28220 Z= 0.267 Chirality : 0.041 0.288 3391 Planarity : 0.004 0.053 3319 Dihedral : 4.652 53.284 2672 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.89 % Allowed : 19.78 % Favored : 78.33 % 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: 0.63 (0.18), residues: 2351 helix: 2.82 (0.20), residues: 729 sheet: 0.21 (0.21), residues: 608 loop : -1.31 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 314 TYR 0.010 0.001 TYR E 234 PHE 0.032 0.001 PHE B 447 TRP 0.015 0.001 TRP A 60 HIS 0.002 0.000 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (20565) covalent geometry : angle 0.54510 / 0.26 (28066) SS BOND : bond 0.00542 / 0.27 ( 11) SS BOND : angle 1.06492 / 0.54 ( 22) hydrogen bonds : bond 0.03716 / 2.44 ( 834) hydrogen bonds : angle 3.42111 / 2.31 ( 2625) link_ALPHA1-3 : bond 0.00818 / 0.45 ( 5) link_ALPHA1-3 : angle 1.36970 / 0.76 ( 15) link_ALPHA1-6 : bond 0.00581 / 0.34 ( 5) link_ALPHA1-6 : angle 1.34488 / 0.75 ( 15) link_BETA1-4 : bond 0.00473 / 0.31 ( 18) link_BETA1-4 : angle 1.38361 / 1.00 ( 54) link_NAG-ASN : bond 0.00492 / 0.30 ( 16) link_NAG-ASN : angle 2.61025 / 1.86 ( 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 367 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 0.796 Fit side-chains REVERT: A 92 LEU cc_start: 0.8341 (pt) cc_final: 0.7835 (tt) REVERT: A 175 GLU cc_start: 0.8347 (tt0) cc_final: 0.8108 (tt0) REVERT: B 31 GLN cc_start: 0.7690 (tt0) cc_final: 0.7138 (tt0) REVERT: B 227 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7391 (mt) REVERT: B 230 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8052 (mm) REVERT: B 231 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8871 (tp) REVERT: B 428 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: C 75 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8281 (ttp-110) REVERT: C 227 LEU cc_start: 0.8972 (tt) cc_final: 0.8206 (mt) REVERT: C 270 ASP cc_start: 0.8013 (t0) cc_final: 0.7812 (t0) REVERT: C 404 GLN cc_start: 0.6877 (tt0) cc_final: 0.6606 (mt0) REVERT: D 83 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8583 (mp10) REVERT: D 291 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (p) REVERT: D 428 ASN cc_start: 0.8014 (t0) cc_final: 0.7663 (m-40) REVERT: D 450 TRP cc_start: 0.7797 (m100) cc_final: 0.7099 (m100) REVERT: D 454 LEU cc_start: 0.7668 (tt) cc_final: 0.6914 (mt) REVERT: E 179 GLU cc_start: 0.8041 (tp30) cc_final: 0.7839 (tp30) REVERT: E 241 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8125 (mp0) REVERT: E 418 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8103 (mtpt) REVERT: E 441 PHE cc_start: 0.8051 (m-80) cc_final: 0.7812 (m-80) REVERT: E 445 PHE cc_start: 0.6564 (m-10) cc_final: 0.6340 (m-80) REVERT: F 101 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7529 (mm-30) REVERT: H 32 ARG cc_start: 0.7563 (mtt180) cc_final: 0.6564 (mmp-170) outliers start: 41 outliers final: 24 residues processed: 352 average time/residue: 0.1391 time to fit residues: 78.2312 Evaluate side-chains 328 residues out of total 2174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 112 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 201 optimal weight: 0.3980 chunk 172 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.098478 restraints weight = 28493.698| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.14 r_work: 0.3058 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20620 Z= 0.151 Angle : 0.625 9.448 28220 Z= 0.298 Chirality : 0.043 0.318 3391 Planarity : 0.004 0.057 3319 Dihedral : 4.775 49.529 2671 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.84 % Allowed : 20.10 % 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: 0.53 (0.18), residues: 2351 helix: 2.60 (0.20), residues: 739 sheet: 0.29 (0.22), residues: 601 loop : -1.39 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 314 TYR 0.016 0.001 TYR E 234 PHE 0.034 0.001 PHE E 323 TRP 0.015 0.001 TRP C 153 HIS 0.003 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (20565) covalent geometry : angle 0.61032 / 0.30 (28066) SS BOND : bond 0.00526 / 0.28 ( 11) SS BOND : angle 1.16580 / 0.65 ( 22) hydrogen bonds : bond 0.04467 / 2.92 ( 834) hydrogen bonds : angle 3.63039 / 2.46 ( 2625) link_ALPHA1-3 : bond 0.00773 / 0.41 ( 5) link_ALPHA1-3 : angle 1.33727 / 0.74 ( 15) link_ALPHA1-6 : bond 0.00560 / 0.30 ( 5) link_ALPHA1-6 : angle 1.33422 / 0.75 ( 15) link_BETA1-4 : bond 0.00441 / 0.30 ( 18) link_BETA1-4 : angle 1.54709 / 1.08 ( 54) link_NAG-ASN : bond 0.00408 / 0.24 ( 16) link_NAG-ASN : angle 2.66405 / 1.92 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5577.39 seconds wall clock time: 96 minutes 12.68 seconds (5772.68 seconds total)