Starting phenix.real_space_refine on Sat Sep 12 13:40:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.map" model { file = "/net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hiq_0227/09_2026/6hiq_0227.cif" } resolution = 3.2 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= 0.001 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10580 2.51 5 N 2595 2.21 5 O 2890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 16110 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" 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: "G" 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: "H" 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: "I" 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: "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: 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: "L" 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: "M" 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: "N" 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: "O" 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: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.72, per 1000 atoms: 0.23 Number of scatterers: 16110 At special positions: 0 Unit cell: (97.097, 94.963, 165.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2890 8.00 N 2595 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 501 " - " ASN D 82 " " NAG E 501 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN E 164 " " NAG I 1 " - " ASN E 148 " " NAG J 1 " - " ASN B 164 " " NAG K 1 " - " ASN B 148 " " NAG L 1 " - " ASN C 164 " " NAG M 1 " - " ASN C 148 " " NAG N 1 " - " ASN D 164 " " NAG O 1 " - " ASN D 148 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 755.8 milliseconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 44.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 176' Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY A 249 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.863A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 460 removed outlier: 3.561A pdb=" N VAL A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.601A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 176' Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 241 removed outlier: 3.503A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY E 249 " --> pdb=" O PRO E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 294 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 332 removed outlier: 3.862A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU E 405 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 436 " --> pdb=" O VAL E 432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 437 " --> pdb=" O LEU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 460 removed outlier: 3.562A pdb=" N VAL E 453 " --> pdb=" O SER E 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.627A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 176' Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 245 through 249 removed outlier: 4.186A pdb=" N GLY B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.863A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 460 removed outlier: 3.562A pdb=" N VAL B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 176' Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY C 249 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 269 " --> pdb=" O PHE C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 removed outlier: 3.862A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 460 removed outlier: 3.561A pdb=" N VAL C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 170 through 176' Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 294 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.863A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 447 removed outlier: 3.980A pdb=" N GLU D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 436 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 437 " --> pdb=" O LEU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 460 removed outlier: 3.561A pdb=" N VAL D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 65 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 164 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 65 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN E 164 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 65 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 164 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 65 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 164 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.128A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.128A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 65 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN D 164 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2190 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: 2.75 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4883 1.34 - 1.46: 3525 1.46 - 1.58: 8067 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 16545 Sorted by residual: bond pdb=" CG SRO B 502 " pdb=" CD2 SRO B 502 " ideal model delta sigma weight residual 1.438 1.358 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" CG SRO D 502 " pdb=" CD2 SRO D 502 " ideal model delta sigma weight residual 1.438 1.358 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CG SRO A 502 " pdb=" CD2 SRO A 502 " ideal model delta sigma weight residual 1.438 1.358 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CG SRO C 502 " pdb=" CD2 SRO C 502 " ideal model delta sigma weight residual 1.438 1.359 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CG SRO E 502 " pdb=" CD2 SRO E 502 " ideal model delta sigma weight residual 1.438 1.359 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 16540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 21782 2.42 - 4.84: 682 4.84 - 7.26: 76 7.26 - 9.68: 50 9.68 - 12.10: 20 Bond angle restraints: 22610 Sorted by residual: angle pdb=" C ILE A 267 " pdb=" N ILE A 268 " pdb=" CA ILE A 268 " ideal model delta sigma weight residual 120.46 126.08 -5.62 1.37e+00 5.33e-01 1.68e+01 angle pdb=" C ILE B 267 " pdb=" N ILE B 268 " pdb=" CA ILE B 268 " ideal model delta sigma weight residual 120.46 126.07 -5.61 1.37e+00 5.33e-01 1.68e+01 angle pdb=" C ILE E 267 " pdb=" N ILE E 268 " pdb=" CA ILE E 268 " ideal model delta sigma weight residual 120.46 126.07 -5.61 1.37e+00 5.33e-01 1.68e+01 angle pdb=" C ILE D 267 " pdb=" N ILE D 268 " pdb=" CA ILE D 268 " ideal model delta sigma weight residual 120.46 126.06 -5.60 1.37e+00 5.33e-01 1.67e+01 angle pdb=" C ILE C 267 " pdb=" N ILE C 268 " pdb=" CA ILE C 268 " ideal model delta sigma weight residual 120.46 126.04 -5.58 1.37e+00 5.33e-01 1.66e+01 ... (remaining 22605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 9095 17.43 - 34.85: 370 34.85 - 52.28: 45 52.28 - 69.70: 10 69.70 - 87.13: 10 Dihedral angle restraints: 9530 sinusoidal: 3790 harmonic: 5740 Sorted by residual: dihedral pdb=" CA GLN D 66 " pdb=" C GLN D 66 " pdb=" N TYR D 67 " pdb=" CA TYR D 67 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA GLN A 66 " pdb=" C GLN A 66 " pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA GLN B 66 " pdb=" C GLN B 66 " pdb=" N TYR B 67 " pdb=" CA TYR B 67 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 9527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1827 0.055 - 0.111: 655 0.111 - 0.166: 168 0.166 - 0.222: 25 0.222 - 0.277: 5 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CB ILE D 139 " pdb=" CA ILE D 139 " pdb=" CG1 ILE D 139 " pdb=" CG2 ILE D 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE C 139 " pdb=" CA ILE C 139 " pdb=" CG1 ILE C 139 " pdb=" CG2 ILE C 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE B 139 " pdb=" CA ILE B 139 " pdb=" CG1 ILE B 139 " pdb=" CG2 ILE B 139 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2677 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " -0.015 2.00e-02 2.50e+03 1.68e-02 7.07e+00 pdb=" CG TRP B 168 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.016 2.00e-02 2.50e+03 1.68e-02 7.05e+00 pdb=" CG TRP C 168 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " -0.015 2.00e-02 2.50e+03 1.68e-02 7.03e+00 pdb=" CG TRP A 168 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.001 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4987 2.84 - 3.35: 14015 3.35 - 3.87: 25879 3.87 - 4.38: 29445 4.38 - 4.90: 50052 Nonbonded interactions: 124378 Sorted by model distance: nonbonded pdb=" OE2 GLU D 53 " pdb=" NH2 ARG D 218 " model vdw 2.319 3.120 nonbonded pdb=" OE2 GLU E 53 " pdb=" NH2 ARG E 218 " model vdw 2.319 3.120 nonbonded pdb=" OE2 GLU A 53 " pdb=" NH2 ARG A 218 " model vdw 2.320 3.120 nonbonded pdb=" OE2 GLU C 53 " pdb=" NH2 ARG C 218 " model vdw 2.320 3.120 nonbonded pdb=" OE2 GLU B 53 " pdb=" NH2 ARG B 218 " model vdw 2.320 3.120 ... (remaining 124373 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.440 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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: 18.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 0.080 16575 Z= 0.300 Angle : 1.084 12.097 22695 Z= 0.529 Chirality : 0.061 0.277 2680 Planarity : 0.006 0.055 2755 Dihedral : 10.602 87.130 5775 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.29 % Allowed : 4.91 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.97 (0.14), residues: 1905 helix: -4.19 (0.09), residues: 685 sheet: -2.40 (0.22), residues: 405 loop : -2.76 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 217 TYR 0.037 0.004 TYR B 116 PHE 0.016 0.002 PHE D 287 TRP 0.044 0.003 TRP B 168 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.30 (16545) covalent geometry : angle 1.08188 / 0.53 (22610) SS BOND : bond 0.00330 / 0.19 ( 5) SS BOND : angle 0.32285 / 0.18 ( 10) hydrogen bonds : bond 0.30332 / 19.93 ( 695) hydrogen bonds : angle 10.21342 / 6.90 ( 2190) link_BETA1-4 : bond 0.00634 / 0.36 ( 10) link_BETA1-4 : angle 1.66798 / 1.16 ( 30) link_NAG-ASN : bond 0.00212 / 0.15 ( 15) link_NAG-ASN : angle 1.77108 / 1.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7843 (t70) cc_final: 0.7531 (t0) REVERT: A 233 PHE cc_start: 0.7750 (t80) cc_final: 0.7309 (t80) REVERT: E 262 TYR cc_start: 0.7478 (t80) cc_final: 0.7243 (t80) REVERT: E 419 MET cc_start: 0.8022 (mmm) cc_final: 0.7465 (tmm) REVERT: B 233 PHE cc_start: 0.7981 (t80) cc_final: 0.7773 (t80) REVERT: B 411 HIS cc_start: 0.8250 (t70) cc_final: 0.7865 (t70) REVERT: B 414 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7432 (tm-30) REVERT: B 419 MET cc_start: 0.8172 (mmm) cc_final: 0.7532 (tmm) REVERT: C 233 PHE cc_start: 0.7844 (t80) cc_final: 0.7515 (t80) REVERT: C 262 TYR cc_start: 0.7651 (t80) cc_final: 0.7384 (t80) REVERT: C 428 ARG cc_start: 0.7017 (mmt180) cc_final: 0.6790 (mpt180) REVERT: D 291 MET cc_start: 0.7258 (ttp) cc_final: 0.6927 (ttp) REVERT: D 419 MET cc_start: 0.7860 (mmm) cc_final: 0.7552 (tmm) outliers start: 5 outliers final: 0 residues processed: 279 average time/residue: 0.1881 time to fit residues: 71.1672 Evaluate side-chains 137 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 130 GLN A 147 GLN A 158 HIS E 118 HIS E 130 GLN E 147 GLN E 158 HIS E 460 HIS B 118 HIS B 130 GLN B 147 GLN B 460 HIS C 118 HIS C 130 GLN C 147 GLN C 460 HIS D 118 HIS D 130 GLN D 147 GLN D 158 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088472 restraints weight = 26389.137| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.07 r_work: 0.2997 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16575 Z= 0.164 Angle : 0.700 7.863 22695 Z= 0.348 Chirality : 0.047 0.159 2680 Planarity : 0.005 0.041 2755 Dihedral : 7.788 86.798 2120 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.43 % Allowed : 9.25 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.96 (0.18), residues: 1905 helix: -1.55 (0.16), residues: 715 sheet: -2.22 (0.21), residues: 475 loop : -1.93 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 428 TYR 0.028 0.002 TYR E 67 PHE 0.020 0.002 PHE D 233 TRP 0.022 0.001 TRP E 168 HIS 0.005 0.001 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16545) covalent geometry : angle 0.69732 / 0.35 (22610) SS BOND : bond 0.00304 / 0.17 ( 5) SS BOND : angle 0.36844 / 0.24 ( 10) hydrogen bonds : bond 0.06004 / 3.94 ( 695) hydrogen bonds : angle 6.00468 / 4.02 ( 2190) link_BETA1-4 : bond 0.00255 / 0.15 ( 10) link_BETA1-4 : angle 1.26445 / 0.82 ( 30) link_NAG-ASN : bond 0.00161 / 0.09 ( 15) link_NAG-ASN : angle 1.19894 / 0.80 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.9067 (tpp) cc_final: 0.8791 (tpp) REVERT: A 262 TYR cc_start: 0.7754 (t80) cc_final: 0.7383 (t80) REVERT: E 262 TYR cc_start: 0.7659 (t80) cc_final: 0.7420 (t80) REVERT: E 291 MET cc_start: 0.7187 (ttp) cc_final: 0.6962 (ttm) REVERT: E 415 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7776 (mmtm) REVERT: E 419 MET cc_start: 0.8253 (mmm) cc_final: 0.7473 (tmm) REVERT: B 250 GLU cc_start: 0.7595 (tt0) cc_final: 0.7381 (tt0) REVERT: B 262 TYR cc_start: 0.7706 (t80) cc_final: 0.7285 (t80) REVERT: C 233 PHE cc_start: 0.7971 (t80) cc_final: 0.7763 (t80) REVERT: D 262 TYR cc_start: 0.7766 (t80) cc_final: 0.7498 (t80) REVERT: D 286 TYR cc_start: 0.8064 (t80) cc_final: 0.7557 (t80) REVERT: D 291 MET cc_start: 0.7644 (ttp) cc_final: 0.7260 (ttp) REVERT: D 410 ARG cc_start: 0.7842 (ptm-80) cc_final: 0.7182 (tmm160) REVERT: D 415 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7433 (mmtm) REVERT: D 418 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7970 (tp30) REVERT: D 419 MET cc_start: 0.7903 (mmm) cc_final: 0.7272 (tmm) outliers start: 42 outliers final: 17 residues processed: 207 average time/residue: 0.1360 time to fit residues: 41.9903 Evaluate side-chains 136 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 187 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 460 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.083938 restraints weight = 26693.247| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.16 r_work: 0.2911 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16575 Z= 0.213 Angle : 0.697 8.686 22695 Z= 0.343 Chirality : 0.047 0.175 2680 Planarity : 0.005 0.033 2755 Dihedral : 7.494 89.044 2120 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.70 % Allowed : 10.69 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.19), residues: 1905 helix: 0.23 (0.19), residues: 715 sheet: -1.94 (0.22), residues: 450 loop : -1.77 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 218 TYR 0.028 0.002 TYR B 67 PHE 0.024 0.002 PHE E 254 TRP 0.020 0.002 TRP E 168 HIS 0.006 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (16545) covalent geometry : angle 0.69286 / 0.34 (22610) SS BOND : bond 0.00516 / 0.30 ( 5) SS BOND : angle 0.89616 / 0.51 ( 10) hydrogen bonds : bond 0.04928 / 3.23 ( 695) hydrogen bonds : angle 5.21586 / 3.51 ( 2190) link_BETA1-4 : bond 0.00373 / 0.21 ( 10) link_BETA1-4 : angle 1.43582 / 0.93 ( 30) link_NAG-ASN : bond 0.00249 / 0.16 ( 15) link_NAG-ASN : angle 1.47011 / 0.97 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 121 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7871 (t80) cc_final: 0.7534 (t80) REVERT: A 315 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7195 (mtt90) REVERT: E 233 PHE cc_start: 0.8210 (t80) cc_final: 0.7980 (t80) REVERT: E 262 TYR cc_start: 0.7670 (t80) cc_final: 0.7465 (t80) REVERT: E 265 PHE cc_start: 0.7812 (t80) cc_final: 0.7454 (t80) REVERT: E 419 MET cc_start: 0.8206 (mmm) cc_final: 0.7400 (tmm) REVERT: B 262 TYR cc_start: 0.7719 (t80) cc_final: 0.7382 (t80) REVERT: B 315 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7345 (mtt180) REVERT: B 428 ARG cc_start: 0.6710 (mpt180) cc_final: 0.6192 (tpt170) REVERT: B 459 TRP cc_start: 0.5815 (OUTLIER) cc_final: 0.5526 (m-10) REVERT: C 233 PHE cc_start: 0.8154 (t80) cc_final: 0.7779 (t80) REVERT: C 262 TYR cc_start: 0.7753 (t80) cc_final: 0.7485 (t80) REVERT: D 250 GLU cc_start: 0.7512 (tt0) cc_final: 0.7302 (pt0) REVERT: D 262 TYR cc_start: 0.7760 (t80) cc_final: 0.7442 (t80) REVERT: D 291 MET cc_start: 0.7660 (ttp) cc_final: 0.7198 (ttp) REVERT: D 298 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8162 (tp) REVERT: D 418 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7812 (tp30) REVERT: D 419 MET cc_start: 0.8073 (mmm) cc_final: 0.7465 (tmm) REVERT: D 424 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7136 (tmm-80) outliers start: 64 outliers final: 28 residues processed: 173 average time/residue: 0.1281 time to fit residues: 33.5434 Evaluate side-chains 144 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 0.0270 chunk 97 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.085982 restraints weight = 26497.941| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.16 r_work: 0.2947 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16575 Z= 0.129 Angle : 0.603 7.386 22695 Z= 0.296 Chirality : 0.044 0.148 2680 Planarity : 0.004 0.030 2755 Dihedral : 6.921 88.248 2120 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.58 % Allowed : 12.31 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1905 helix: 1.09 (0.20), residues: 715 sheet: -2.00 (0.22), residues: 430 loop : -1.65 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 439 TYR 0.024 0.002 TYR A 67 PHE 0.022 0.001 PHE A 233 TRP 0.013 0.001 TRP D 168 HIS 0.002 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16545) covalent geometry : angle 0.60032 / 0.30 (22610) SS BOND : bond 0.00345 / 0.20 ( 5) SS BOND : angle 0.67960 / 0.40 ( 10) hydrogen bonds : bond 0.04042 / 2.65 ( 695) hydrogen bonds : angle 4.91055 / 3.31 ( 2190) link_BETA1-4 : bond 0.00301 / 0.17 ( 10) link_BETA1-4 : angle 1.15950 / 0.76 ( 30) link_NAG-ASN : bond 0.00123 / 0.07 ( 15) link_NAG-ASN : angle 1.19760 / 0.80 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 134 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7832 (t80) cc_final: 0.7528 (t80) REVERT: A 315 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7220 (mtt90) REVERT: E 129 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8630 (pp) REVERT: E 262 TYR cc_start: 0.7674 (t80) cc_final: 0.7408 (t80) REVERT: E 265 PHE cc_start: 0.7729 (t80) cc_final: 0.7462 (t80) REVERT: E 418 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7892 (tp30) REVERT: E 419 MET cc_start: 0.8152 (mmm) cc_final: 0.7249 (tmm) REVERT: B 262 TYR cc_start: 0.7560 (t80) cc_final: 0.7299 (t80) REVERT: B 315 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7309 (mtt180) REVERT: B 428 ARG cc_start: 0.6589 (mpt180) cc_final: 0.6113 (tpt170) REVERT: B 459 TRP cc_start: 0.5912 (OUTLIER) cc_final: 0.5630 (m-10) REVERT: C 129 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8738 (pp) REVERT: C 233 PHE cc_start: 0.8137 (t80) cc_final: 0.7768 (t80) REVERT: C 428 ARG cc_start: 0.6321 (mpt180) cc_final: 0.5467 (mmt-90) REVERT: D 262 TYR cc_start: 0.7746 (t80) cc_final: 0.7498 (t80) REVERT: D 291 MET cc_start: 0.7650 (ttp) cc_final: 0.7186 (ttp) REVERT: D 298 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7914 (tp) REVERT: D 418 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7779 (tp30) REVERT: D 419 MET cc_start: 0.8065 (mmm) cc_final: 0.7502 (tmm) REVERT: D 424 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7080 (tmm-80) REVERT: D 459 TRP cc_start: 0.6069 (OUTLIER) cc_final: 0.5644 (m-10) outliers start: 62 outliers final: 27 residues processed: 185 average time/residue: 0.1204 time to fit residues: 34.6615 Evaluate side-chains 145 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 118 optimal weight: 0.0370 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 171 optimal weight: 0.0980 chunk 134 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.085840 restraints weight = 26387.168| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.09 r_work: 0.2948 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16575 Z= 0.128 Angle : 0.591 9.770 22695 Z= 0.290 Chirality : 0.044 0.150 2680 Planarity : 0.004 0.027 2755 Dihedral : 6.374 85.980 2120 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.29 % Allowed : 12.49 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.20), residues: 1905 helix: 1.58 (0.20), residues: 715 sheet: -1.90 (0.23), residues: 430 loop : -1.61 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 439 TYR 0.022 0.002 TYR B 67 PHE 0.023 0.001 PHE C 254 TRP 0.012 0.001 TRP C 156 HIS 0.002 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16545) covalent geometry : angle 0.58799 / 0.29 (22610) SS BOND : bond 0.00334 / 0.19 ( 5) SS BOND : angle 0.68832 / 0.38 ( 10) hydrogen bonds : bond 0.03750 / 2.47 ( 695) hydrogen bonds : angle 4.75745 / 3.21 ( 2190) link_BETA1-4 : bond 0.00253 / 0.15 ( 10) link_BETA1-4 : angle 1.22217 / 0.80 ( 30) link_NAG-ASN : bond 0.00104 / 0.06 ( 15) link_NAG-ASN : angle 1.22025 / 0.81 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 125 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7822 (t80) cc_final: 0.7510 (t80) REVERT: A 315 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7229 (mtt90) REVERT: E 129 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8672 (pp) REVERT: E 235 MET cc_start: 0.8672 (mmm) cc_final: 0.8470 (mmp) REVERT: E 262 TYR cc_start: 0.7893 (t80) cc_final: 0.7478 (t80) REVERT: B 215 ILE cc_start: 0.9019 (pt) cc_final: 0.8772 (pt) REVERT: B 262 TYR cc_start: 0.7615 (t80) cc_final: 0.7398 (t80) REVERT: B 291 MET cc_start: 0.7392 (ttp) cc_final: 0.7167 (ttp) REVERT: B 315 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7267 (mtt180) REVERT: B 428 ARG cc_start: 0.6471 (mpt180) cc_final: 0.5661 (mmt-90) REVERT: B 438 PHE cc_start: 0.7886 (t80) cc_final: 0.7649 (t80) REVERT: B 459 TRP cc_start: 0.5942 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: C 129 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8876 (pp) REVERT: C 233 PHE cc_start: 0.8169 (t80) cc_final: 0.7848 (t80) REVERT: C 315 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7229 (mtt90) REVERT: C 428 ARG cc_start: 0.6286 (mpt180) cc_final: 0.5438 (mmt-90) REVERT: D 262 TYR cc_start: 0.7850 (t80) cc_final: 0.7548 (t80) REVERT: D 291 MET cc_start: 0.7676 (ttp) cc_final: 0.7173 (ttp) REVERT: D 298 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7951 (tp) REVERT: D 418 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8026 (tp30) REVERT: D 419 MET cc_start: 0.8144 (mmm) cc_final: 0.7518 (tmm) REVERT: D 459 TRP cc_start: 0.6210 (OUTLIER) cc_final: 0.5767 (m-10) outliers start: 57 outliers final: 33 residues processed: 172 average time/residue: 0.1320 time to fit residues: 34.8738 Evaluate side-chains 151 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.0060 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 73 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 65 optimal weight: 0.0170 overall best weight: 0.8236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.086791 restraints weight = 26162.526| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.08 r_work: 0.2955 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16575 Z= 0.115 Angle : 0.569 8.745 22695 Z= 0.280 Chirality : 0.044 0.168 2680 Planarity : 0.004 0.026 2755 Dihedral : 5.714 83.105 2120 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.12 % Allowed : 13.41 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.20), residues: 1905 helix: 1.99 (0.20), residues: 710 sheet: -1.79 (0.22), residues: 475 loop : -1.40 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 428 TYR 0.023 0.002 TYR E 448 PHE 0.026 0.001 PHE A 254 TRP 0.011 0.001 TRP C 156 HIS 0.002 0.000 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (16545) covalent geometry : angle 0.56624 / 0.28 (22610) SS BOND : bond 0.00293 / 0.18 ( 5) SS BOND : angle 0.66440 / 0.38 ( 10) hydrogen bonds : bond 0.03454 / 2.29 ( 695) hydrogen bonds : angle 4.61495 / 3.11 ( 2190) link_BETA1-4 : bond 0.00298 / 0.17 ( 10) link_BETA1-4 : angle 1.16073 / 0.77 ( 30) link_NAG-ASN : bond 0.00123 / 0.07 ( 15) link_NAG-ASN : angle 1.13188 / 0.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7822 (t80) cc_final: 0.7501 (t80) REVERT: A 315 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7332 (mtt90) REVERT: E 129 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8727 (pp) REVERT: E 215 ILE cc_start: 0.8914 (pt) cc_final: 0.8689 (pt) REVERT: E 235 MET cc_start: 0.8741 (mmm) cc_final: 0.8409 (mmm) REVERT: E 262 TYR cc_start: 0.7886 (t80) cc_final: 0.7489 (t80) REVERT: E 315 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7267 (mtt90) REVERT: B 215 ILE cc_start: 0.8900 (pt) cc_final: 0.8677 (pt) REVERT: B 262 TYR cc_start: 0.7602 (t80) cc_final: 0.7397 (t80) REVERT: B 291 MET cc_start: 0.7309 (ttp) cc_final: 0.7094 (ttp) REVERT: B 315 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7273 (mtt180) REVERT: B 428 ARG cc_start: 0.6324 (mpt180) cc_final: 0.6081 (tpt170) REVERT: B 438 PHE cc_start: 0.7793 (t80) cc_final: 0.7592 (t80) REVERT: B 459 TRP cc_start: 0.5985 (OUTLIER) cc_final: 0.5670 (m-10) REVERT: C 129 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8753 (pp) REVERT: C 233 PHE cc_start: 0.8219 (t80) cc_final: 0.7993 (t80) REVERT: C 315 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7127 (mtt180) REVERT: C 428 ARG cc_start: 0.6214 (mpt180) cc_final: 0.5380 (mmt-90) REVERT: D 262 TYR cc_start: 0.7839 (t80) cc_final: 0.7568 (t80) REVERT: D 291 MET cc_start: 0.7708 (ttp) cc_final: 0.7185 (ttp) REVERT: D 298 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7805 (tp) REVERT: D 459 TRP cc_start: 0.5998 (OUTLIER) cc_final: 0.5665 (m-10) outliers start: 54 outliers final: 39 residues processed: 163 average time/residue: 0.1332 time to fit residues: 33.0737 Evaluate side-chains 153 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 115 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.087439 restraints weight = 26355.807| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.24 r_work: 0.2945 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16575 Z= 0.113 Angle : 0.566 8.206 22695 Z= 0.277 Chirality : 0.043 0.145 2680 Planarity : 0.004 0.026 2755 Dihedral : 5.291 79.346 2120 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.24 % Allowed : 14.05 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1905 helix: 2.23 (0.20), residues: 710 sheet: -1.71 (0.23), residues: 450 loop : -1.43 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 439 TYR 0.024 0.001 TYR E 448 PHE 0.024 0.001 PHE E 254 TRP 0.011 0.001 TRP C 156 HIS 0.001 0.000 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (16545) covalent geometry : angle 0.56265 / 0.28 (22610) SS BOND : bond 0.00276 / 0.16 ( 5) SS BOND : angle 0.65474 / 0.37 ( 10) hydrogen bonds : bond 0.03298 / 2.16 ( 695) hydrogen bonds : angle 4.54019 / 3.07 ( 2190) link_BETA1-4 : bond 0.00312 / 0.18 ( 10) link_BETA1-4 : angle 1.19123 / 0.79 ( 30) link_NAG-ASN : bond 0.00115 / 0.07 ( 15) link_NAG-ASN : angle 1.15556 / 0.77 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7815 (t80) cc_final: 0.7496 (t80) REVERT: A 315 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7329 (mtt90) REVERT: E 105 ASP cc_start: 0.8330 (p0) cc_final: 0.8034 (p0) REVERT: E 129 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8748 (pp) REVERT: E 235 MET cc_start: 0.8735 (mmm) cc_final: 0.8382 (mmm) REVERT: E 262 TYR cc_start: 0.7849 (t80) cc_final: 0.7481 (t80) REVERT: E 315 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7278 (mtt90) REVERT: B 215 ILE cc_start: 0.8851 (pt) cc_final: 0.8615 (pt) REVERT: B 262 TYR cc_start: 0.7633 (t80) cc_final: 0.7408 (t80) REVERT: B 291 MET cc_start: 0.7329 (ttp) cc_final: 0.7105 (ttp) REVERT: B 315 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7315 (mtt180) REVERT: B 428 ARG cc_start: 0.6415 (mpt180) cc_final: 0.5762 (mmt-90) REVERT: B 438 PHE cc_start: 0.7784 (t80) cc_final: 0.7560 (t80) REVERT: B 459 TRP cc_start: 0.6111 (OUTLIER) cc_final: 0.5773 (m-10) REVERT: C 129 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8797 (pp) REVERT: C 315 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7164 (mtt180) REVERT: C 428 ARG cc_start: 0.6158 (mpt180) cc_final: 0.5345 (mmt-90) REVERT: D 291 MET cc_start: 0.7705 (ttp) cc_final: 0.7219 (ttp) REVERT: D 459 TRP cc_start: 0.6011 (OUTLIER) cc_final: 0.5719 (m-10) outliers start: 56 outliers final: 37 residues processed: 161 average time/residue: 0.1314 time to fit residues: 32.1945 Evaluate side-chains 156 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 2 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 132 optimal weight: 0.4980 chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087863 restraints weight = 26004.208| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.06 r_work: 0.2971 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16575 Z= 0.103 Angle : 0.560 9.383 22695 Z= 0.272 Chirality : 0.043 0.133 2680 Planarity : 0.003 0.025 2755 Dihedral : 4.947 72.058 2120 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.77 % Allowed : 14.86 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1905 helix: 2.42 (0.20), residues: 710 sheet: -1.88 (0.22), residues: 455 loop : -1.23 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 439 TYR 0.024 0.001 TYR E 448 PHE 0.027 0.001 PHE C 233 TRP 0.010 0.001 TRP C 168 HIS 0.002 0.000 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (16545) covalent geometry : angle 0.55737 / 0.27 (22610) SS BOND : bond 0.00262 / 0.15 ( 5) SS BOND : angle 0.65989 / 0.38 ( 10) hydrogen bonds : bond 0.03127 / 2.05 ( 695) hydrogen bonds : angle 4.41042 / 2.99 ( 2190) link_BETA1-4 : bond 0.00320 / 0.18 ( 10) link_BETA1-4 : angle 1.13571 / 0.76 ( 30) link_NAG-ASN : bond 0.00139 / 0.08 ( 15) link_NAG-ASN : angle 1.08943 / 0.73 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.8176 (t80) cc_final: 0.7884 (t80) REVERT: A 262 TYR cc_start: 0.7865 (t80) cc_final: 0.7543 (t80) REVERT: A 291 MET cc_start: 0.7601 (ttt) cc_final: 0.7290 (ttp) REVERT: A 315 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7274 (mtt90) REVERT: E 129 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8742 (pp) REVERT: E 262 TYR cc_start: 0.7896 (t80) cc_final: 0.7691 (t80) REVERT: E 315 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7225 (mtt90) REVERT: B 215 ILE cc_start: 0.8836 (pt) cc_final: 0.8617 (pt) REVERT: B 262 TYR cc_start: 0.7679 (t80) cc_final: 0.7421 (t80) REVERT: B 291 MET cc_start: 0.7539 (ttp) cc_final: 0.7274 (ttp) REVERT: B 315 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7281 (mtt180) REVERT: B 428 ARG cc_start: 0.6391 (mpt180) cc_final: 0.5788 (mmt-90) REVERT: B 438 PHE cc_start: 0.7827 (t80) cc_final: 0.7615 (t80) REVERT: B 459 TRP cc_start: 0.6008 (OUTLIER) cc_final: 0.5722 (m-10) REVERT: C 129 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8755 (pp) REVERT: C 315 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7070 (mtt180) REVERT: C 428 ARG cc_start: 0.6208 (mpt180) cc_final: 0.5036 (mmt180) REVERT: D 459 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.5749 (m-10) outliers start: 48 outliers final: 35 residues processed: 164 average time/residue: 0.1282 time to fit residues: 32.0308 Evaluate side-chains 158 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 151 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.122415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.085383 restraints weight = 26382.652| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.17 r_work: 0.2931 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16575 Z= 0.131 Angle : 0.569 7.821 22695 Z= 0.280 Chirality : 0.044 0.141 2680 Planarity : 0.004 0.026 2755 Dihedral : 4.910 66.212 2120 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.72 % Allowed : 15.14 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.20), residues: 1905 helix: 2.52 (0.20), residues: 710 sheet: -1.97 (0.22), residues: 450 loop : -1.12 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.024 0.002 TYR E 448 PHE 0.028 0.002 PHE E 254 TRP 0.011 0.001 TRP C 156 HIS 0.002 0.001 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (16545) covalent geometry : angle 0.56539 / 0.28 (22610) SS BOND : bond 0.00327 / 0.19 ( 5) SS BOND : angle 0.68247 / 0.39 ( 10) hydrogen bonds : bond 0.03235 / 2.13 ( 695) hydrogen bonds : angle 4.41636 / 3.00 ( 2190) link_BETA1-4 : bond 0.00282 / 0.16 ( 10) link_BETA1-4 : angle 1.23235 / 0.80 ( 30) link_NAG-ASN : bond 0.00103 / 0.06 ( 15) link_NAG-ASN : angle 1.18420 / 0.79 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.8187 (t80) cc_final: 0.7912 (t80) REVERT: A 262 TYR cc_start: 0.7852 (t80) cc_final: 0.7586 (t80) REVERT: A 291 MET cc_start: 0.7582 (ttt) cc_final: 0.7267 (ttp) REVERT: A 315 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7341 (mtt90) REVERT: E 129 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8743 (pp) REVERT: E 262 TYR cc_start: 0.8159 (t80) cc_final: 0.7574 (t80) REVERT: E 291 MET cc_start: 0.8229 (tpp) cc_final: 0.7943 (tpp) REVERT: E 315 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7240 (mtt90) REVERT: E 428 ARG cc_start: 0.6607 (mpt180) cc_final: 0.5919 (mmt-90) REVERT: B 215 ILE cc_start: 0.8871 (pt) cc_final: 0.8636 (pt) REVERT: B 262 TYR cc_start: 0.7552 (t80) cc_final: 0.7269 (t80) REVERT: B 291 MET cc_start: 0.7593 (ttp) cc_final: 0.7309 (ttp) REVERT: B 315 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7342 (mtt180) REVERT: B 428 ARG cc_start: 0.6392 (mpt180) cc_final: 0.5718 (mmt-90) REVERT: B 459 TRP cc_start: 0.6119 (OUTLIER) cc_final: 0.5767 (m-10) REVERT: C 129 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8821 (pp) REVERT: C 315 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7087 (mtt180) REVERT: C 428 ARG cc_start: 0.6236 (mpt180) cc_final: 0.5081 (mmt180) REVERT: D 459 TRP cc_start: 0.6066 (OUTLIER) cc_final: 0.5766 (m-10) outliers start: 47 outliers final: 36 residues processed: 150 average time/residue: 0.1301 time to fit residues: 29.3666 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 33 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 0.0970 chunk 168 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.086484 restraints weight = 26032.071| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.07 r_work: 0.2946 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16575 Z= 0.120 Angle : 0.570 7.605 22695 Z= 0.280 Chirality : 0.044 0.161 2680 Planarity : 0.004 0.027 2755 Dihedral : 4.777 57.568 2120 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.60 % Allowed : 15.20 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1905 helix: 2.56 (0.20), residues: 710 sheet: -1.98 (0.22), residues: 450 loop : -1.08 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.024 0.002 TYR E 448 PHE 0.026 0.001 PHE E 254 TRP 0.011 0.001 TRP C 156 HIS 0.002 0.000 HIS D 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (16545) covalent geometry : angle 0.56657 / 0.28 (22610) SS BOND : bond 0.00287 / 0.17 ( 5) SS BOND : angle 0.63735 / 0.36 ( 10) hydrogen bonds : bond 0.03218 / 2.11 ( 695) hydrogen bonds : angle 4.39413 / 2.98 ( 2190) link_BETA1-4 : bond 0.00283 / 0.17 ( 10) link_BETA1-4 : angle 1.17307 / 0.77 ( 30) link_NAG-ASN : bond 0.00111 / 0.06 ( 15) link_NAG-ASN : angle 1.16047 / 0.78 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 233 PHE cc_start: 0.8134 (t80) cc_final: 0.7882 (t80) REVERT: A 262 TYR cc_start: 0.7838 (t80) cc_final: 0.7530 (t80) REVERT: A 291 MET cc_start: 0.7605 (ttt) cc_final: 0.7291 (ttp) REVERT: A 315 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7364 (mtt90) REVERT: E 129 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8727 (pp) REVERT: E 235 MET cc_start: 0.8806 (mmm) cc_final: 0.8467 (mmm) REVERT: E 262 TYR cc_start: 0.8151 (t80) cc_final: 0.7648 (t80) REVERT: E 315 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7229 (mtt90) REVERT: E 428 ARG cc_start: 0.6558 (mpt180) cc_final: 0.5895 (mmt-90) REVERT: B 215 ILE cc_start: 0.8854 (pt) cc_final: 0.8619 (pt) REVERT: B 262 TYR cc_start: 0.7537 (t80) cc_final: 0.7255 (t80) REVERT: B 291 MET cc_start: 0.7548 (ttp) cc_final: 0.7263 (ttp) REVERT: B 315 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7310 (mtt180) REVERT: B 428 ARG cc_start: 0.6362 (mpt180) cc_final: 0.5702 (mmt-90) REVERT: B 459 TRP cc_start: 0.6094 (OUTLIER) cc_final: 0.5701 (m-10) REVERT: C 129 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8793 (pp) REVERT: C 315 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7098 (mtt180) REVERT: C 428 ARG cc_start: 0.6241 (mpt180) cc_final: 0.5132 (mmt180) REVERT: D 459 TRP cc_start: 0.6148 (OUTLIER) cc_final: 0.5791 (m-10) outliers start: 45 outliers final: 34 residues processed: 150 average time/residue: 0.1463 time to fit residues: 32.6384 Evaluate side-chains 155 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 159 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 77 optimal weight: 0.0030 chunk 123 optimal weight: 0.0970 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.087151 restraints weight = 26282.610| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.17 r_work: 0.2963 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16575 Z= 0.101 Angle : 0.557 8.518 22695 Z= 0.272 Chirality : 0.043 0.148 2680 Planarity : 0.003 0.026 2755 Dihedral : 4.476 41.297 2120 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 15.43 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.21), residues: 1905 helix: 2.63 (0.20), residues: 710 sheet: -1.98 (0.22), residues: 450 loop : -1.04 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 428 TYR 0.023 0.001 TYR E 448 PHE 0.030 0.001 PHE B 233 TRP 0.010 0.001 TRP C 156 HIS 0.002 0.000 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (16545) covalent geometry : angle 0.55447 / 0.27 (22610) SS BOND : bond 0.00232 / 0.13 ( 5) SS BOND : angle 0.58815 / 0.34 ( 10) hydrogen bonds : bond 0.03005 / 1.98 ( 695) hydrogen bonds : angle 4.30773 / 2.92 ( 2190) link_BETA1-4 : bond 0.00303 / 0.17 ( 10) link_BETA1-4 : angle 1.12248 / 0.74 ( 30) link_NAG-ASN : bond 0.00127 / 0.07 ( 15) link_NAG-ASN : angle 1.09811 / 0.73 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4166.15 seconds wall clock time: 72 minutes 13.67 seconds (4333.67 seconds total)