Starting phenix.real_space_refine on Sat Jun 14 13:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hiq_0227/06_2025/6hiq_0227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hiq_0227/06_2025/6hiq_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_0227/06_2025/6hiq_0227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hiq_0227/06_2025/6hiq_0227.map" model { file = "/net/cci-nas-00/data/ceres_data/6hiq_0227/06_2025/6hiq_0227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hiq_0227/06_2025/6hiq_0227.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.80, per 1000 atoms: 0.67 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: 4.81 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.56 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: 6.52 Time building geometry restraints manager: 5.20 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: 9570 17.43 - 34.85: 390 34.85 - 52.28: 65 52.28 - 69.70: 20 69.70 - 87.13: 10 Dihedral angle restraints: 10055 sinusoidal: 4315 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 10052 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: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 78.790 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 42.380 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 10.850 87.130 6300 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.044 0.003 TRP B 168 HIS 0.005 0.001 HIS B 119 PHE 0.016 0.002 PHE D 287 TYR 0.037 0.004 TYR B 116 ARG 0.004 0.001 ARG D 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.77108 ( 45) link_BETA1-4 : bond 0.00634 ( 10) link_BETA1-4 : angle 1.66798 ( 30) hydrogen bonds : bond 0.30332 ( 695) hydrogen bonds : angle 10.21342 ( 2190) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.32285 ( 10) covalent geometry : bond 0.00687 (16545) covalent geometry : angle 1.08188 (22610) *********************** 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 : 2.025 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: 0.4506 time to fit residues: 169.9847 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 : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.5980 chunk 144 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089323 restraints weight = 26585.893| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.16 r_work: 0.3001 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16575 Z= 0.154 Angle : 0.697 8.342 22695 Z= 0.347 Chirality : 0.046 0.156 2680 Planarity : 0.005 0.044 2755 Dihedral : 8.741 86.674 2645 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.37 % Allowed : 9.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.17), residues: 1905 helix: -1.56 (0.16), residues: 715 sheet: -2.31 (0.21), residues: 490 loop : -1.94 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 168 HIS 0.004 0.001 HIS D 411 PHE 0.023 0.001 PHE D 233 TYR 0.028 0.002 TYR E 67 ARG 0.004 0.001 ARG A 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 15) link_NAG-ASN : angle 1.11351 ( 45) link_BETA1-4 : bond 0.00325 ( 10) link_BETA1-4 : angle 1.17198 ( 30) hydrogen bonds : bond 0.06383 ( 695) hydrogen bonds : angle 6.07688 ( 2190) SS BOND : bond 0.00427 ( 5) SS BOND : angle 0.61563 ( 10) covalent geometry : bond 0.00325 (16545) covalent geometry : angle 0.69496 (22610) *********************** 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 211 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.9030 (tpp) cc_final: 0.8797 (tpp) REVERT: A 262 TYR cc_start: 0.7706 (t80) cc_final: 0.7349 (t80) REVERT: A 291 MET cc_start: 0.7561 (ttm) cc_final: 0.7244 (ttp) REVERT: E 250 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7162 (pt0) REVERT: E 262 TYR cc_start: 0.7622 (t80) cc_final: 0.7392 (t80) REVERT: E 286 TYR cc_start: 0.7850 (t80) cc_final: 0.7610 (t80) REVERT: E 415 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7777 (mmtm) REVERT: E 419 MET cc_start: 0.8236 (mmm) cc_final: 0.7506 (tmm) REVERT: B 262 TYR cc_start: 0.7629 (t80) cc_final: 0.7315 (t80) REVERT: D 262 TYR cc_start: 0.7757 (t80) cc_final: 0.7484 (t80) REVERT: D 286 TYR cc_start: 0.8027 (t80) cc_final: 0.7564 (t80) REVERT: D 291 MET cc_start: 0.7632 (ttp) cc_final: 0.7251 (ttp) REVERT: D 410 ARG cc_start: 0.7815 (ptm-80) cc_final: 0.7162 (tmm160) REVERT: D 415 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7488 (mmtm) REVERT: D 418 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8016 (tp30) REVERT: D 419 MET cc_start: 0.7886 (mmm) cc_final: 0.7242 (tmm) outliers start: 41 outliers final: 15 residues processed: 202 average time/residue: 0.2811 time to fit residues: 84.7884 Evaluate side-chains 134 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 E residue 250 GLU Chi-restraints excluded: chain E residue 459 TRP 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 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 130 optimal weight: 0.6980 chunk 185 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 92 optimal weight: 0.0370 chunk 114 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS E 460 HIS C 460 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.123815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087480 restraints weight = 26254.751| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.15 r_work: 0.2971 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16575 Z= 0.153 Angle : 0.641 7.310 22695 Z= 0.316 Chirality : 0.045 0.191 2680 Planarity : 0.004 0.032 2755 Dihedral : 7.938 87.523 2645 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.29 % Allowed : 11.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.19), residues: 1905 helix: 0.07 (0.19), residues: 720 sheet: -2.03 (0.22), residues: 475 loop : -1.79 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 168 HIS 0.003 0.001 HIS A 460 PHE 0.017 0.001 PHE A 233 TYR 0.026 0.002 TYR B 67 ARG 0.004 0.000 ARG C 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 15) link_NAG-ASN : angle 1.15709 ( 45) link_BETA1-4 : bond 0.00389 ( 10) link_BETA1-4 : angle 1.22316 ( 30) hydrogen bonds : bond 0.04781 ( 695) hydrogen bonds : angle 5.25891 ( 2190) SS BOND : bond 0.00445 ( 5) SS BOND : angle 0.77422 ( 10) covalent geometry : bond 0.00350 (16545) covalent geometry : angle 0.63855 (22610) *********************** 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 183 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7810 (t80) cc_final: 0.7474 (t80) REVERT: A 291 MET cc_start: 0.7694 (ttm) cc_final: 0.7435 (ttp) REVERT: A 315 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7319 (mtt90) REVERT: E 250 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7266 (pt0) REVERT: E 262 TYR cc_start: 0.7602 (t80) cc_final: 0.7378 (t80) REVERT: E 291 MET cc_start: 0.7003 (ttp) cc_final: 0.6725 (ttm) REVERT: E 419 MET cc_start: 0.8245 (mmm) cc_final: 0.7411 (tmm) REVERT: B 315 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7381 (mtt180) REVERT: B 428 ARG cc_start: 0.6681 (mpt180) cc_final: 0.6163 (tpt170) REVERT: C 106 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7516 (m) REVERT: C 262 TYR cc_start: 0.7774 (t80) cc_final: 0.7461 (t80) REVERT: D 262 TYR cc_start: 0.7685 (t80) cc_final: 0.7369 (t80) REVERT: D 298 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8074 (tp) REVERT: D 410 ARG cc_start: 0.8021 (ptm-80) cc_final: 0.7237 (tmm160) REVERT: D 418 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7728 (tp30) REVERT: D 419 MET cc_start: 0.7995 (mmm) cc_final: 0.7403 (tmm) outliers start: 57 outliers final: 20 residues processed: 170 average time/residue: 0.2867 time to fit residues: 73.4094 Evaluate side-chains 137 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 250 GLU 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 315 ARG Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 106 VAL 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 298 LEU 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 4 optimal weight: 0.0270 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.089702 restraints weight = 25957.967| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.05 r_work: 0.3014 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16575 Z= 0.111 Angle : 0.579 8.597 22695 Z= 0.285 Chirality : 0.044 0.154 2680 Planarity : 0.004 0.029 2755 Dihedral : 6.993 84.042 2645 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.89 % Allowed : 12.31 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.20), residues: 1905 helix: 1.09 (0.19), residues: 715 sheet: -2.05 (0.22), residues: 455 loop : -1.64 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 168 HIS 0.002 0.001 HIS D 411 PHE 0.026 0.001 PHE D 254 TYR 0.024 0.002 TYR A 67 ARG 0.004 0.000 ARG C 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.00333 ( 45) link_BETA1-4 : bond 0.00381 ( 10) link_BETA1-4 : angle 1.06327 ( 30) hydrogen bonds : bond 0.03891 ( 695) hydrogen bonds : angle 4.81883 ( 2190) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.67333 ( 10) covalent geometry : bond 0.00235 (16545) covalent geometry : angle 0.57648 (22610) *********************** 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 197 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 147 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7770 (t80) cc_final: 0.7448 (t80) REVERT: A 291 MET cc_start: 0.7679 (ttm) cc_final: 0.7393 (ttm) REVERT: A 315 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7318 (mtt90) REVERT: E 233 PHE cc_start: 0.8201 (t80) cc_final: 0.7895 (t80) REVERT: E 262 TYR cc_start: 0.7721 (t80) cc_final: 0.7467 (t80) REVERT: E 265 PHE cc_start: 0.7782 (t80) cc_final: 0.7526 (t80) REVERT: E 291 MET cc_start: 0.7096 (ttp) cc_final: 0.6864 (ttt) REVERT: E 418 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7881 (tp30) REVERT: E 419 MET cc_start: 0.8167 (mmm) cc_final: 0.7266 (tmm) REVERT: E 424 ARG cc_start: 0.6578 (tpt170) cc_final: 0.6118 (tmm-80) REVERT: B 315 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7221 (mtt180) REVERT: B 428 ARG cc_start: 0.6382 (mpt180) cc_final: 0.5924 (tpt170) REVERT: C 129 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8812 (pp) REVERT: C 233 PHE cc_start: 0.8145 (t80) cc_final: 0.7941 (t80) REVERT: C 262 TYR cc_start: 0.7838 (t80) cc_final: 0.7557 (t80) REVERT: C 315 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7232 (mtt90) REVERT: C 428 ARG cc_start: 0.6332 (mpt180) cc_final: 0.5452 (mmt-90) REVERT: D 262 TYR cc_start: 0.7644 (t80) cc_final: 0.7407 (t80) REVERT: D 298 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7990 (tp) REVERT: D 418 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7687 (tp30) REVERT: D 419 MET cc_start: 0.8053 (mmm) cc_final: 0.7497 (tmm) REVERT: D 459 TRP cc_start: 0.5980 (OUTLIER) cc_final: 0.5493 (m-10) outliers start: 50 outliers final: 17 residues processed: 185 average time/residue: 0.2772 time to fit residues: 76.5391 Evaluate side-chains 135 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 304 ILE 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 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 315 ARG 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 221 LEU 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 459 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 48 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 10 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.119726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082268 restraints weight = 26829.528| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.16 r_work: 0.2882 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16575 Z= 0.242 Angle : 0.678 8.158 22695 Z= 0.335 Chirality : 0.048 0.186 2680 Planarity : 0.004 0.029 2755 Dihedral : 7.117 86.727 2645 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.93 % Allowed : 12.37 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1905 helix: 1.47 (0.20), residues: 715 sheet: -1.93 (0.23), residues: 430 loop : -1.64 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 168 HIS 0.006 0.001 HIS D 119 PHE 0.027 0.002 PHE D 153 TYR 0.025 0.002 TYR D 67 ARG 0.005 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 15) link_NAG-ASN : angle 1.26306 ( 45) link_BETA1-4 : bond 0.00338 ( 10) link_BETA1-4 : angle 1.43459 ( 30) hydrogen bonds : bond 0.04234 ( 695) hydrogen bonds : angle 4.91520 ( 2190) SS BOND : bond 0.00492 ( 5) SS BOND : angle 0.82995 ( 10) covalent geometry : bond 0.00589 (16545) covalent geometry : angle 0.67457 (22610) *********************** 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 183 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 115 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: A 291 MET cc_start: 0.7802 (ttm) cc_final: 0.7362 (tpp) REVERT: A 315 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7295 (mtt90) REVERT: E 129 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8624 (pp) REVERT: E 262 TYR cc_start: 0.7851 (t80) cc_final: 0.7524 (t80) REVERT: E 265 PHE cc_start: 0.7730 (t80) cc_final: 0.7473 (t80) REVERT: E 291 MET cc_start: 0.7308 (ttp) cc_final: 0.6985 (ttm) REVERT: E 418 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7912 (tp30) REVERT: E 419 MET cc_start: 0.8186 (mmm) cc_final: 0.7333 (tmm) REVERT: B 315 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7328 (mtt180) REVERT: B 428 ARG cc_start: 0.6512 (mpt180) cc_final: 0.6076 (tpt170) REVERT: B 459 TRP cc_start: 0.5220 (m-10) cc_final: 0.4971 (m-10) REVERT: C 262 TYR cc_start: 0.7822 (t80) cc_final: 0.7587 (t80) REVERT: C 315 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7194 (mtt180) REVERT: C 428 ARG cc_start: 0.6393 (mpt180) cc_final: 0.5604 (mmt-90) REVERT: D 250 GLU cc_start: 0.7590 (tt0) cc_final: 0.7305 (pt0) REVERT: D 262 TYR cc_start: 0.7832 (t80) cc_final: 0.7619 (t80) REVERT: D 418 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8034 (tp30) REVERT: D 419 MET cc_start: 0.8091 (mmm) cc_final: 0.7502 (tmm) REVERT: D 459 TRP cc_start: 0.6080 (OUTLIER) cc_final: 0.5657 (m-10) outliers start: 68 outliers final: 42 residues processed: 176 average time/residue: 0.2857 time to fit residues: 74.8884 Evaluate side-chains 151 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain A residue 315 ARG 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 167 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 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 304 ILE 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 180 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 304 ILE 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 C residue 59 THR 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 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 129 LEU 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 264 VAL Chi-restraints excluded: chain D residue 304 ILE 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 32 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.085726 restraints weight = 26263.606| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.09 r_work: 0.2944 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16575 Z= 0.119 Angle : 0.576 7.612 22695 Z= 0.283 Chirality : 0.044 0.138 2680 Planarity : 0.004 0.027 2755 Dihedral : 6.366 85.045 2645 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.72 % Allowed : 13.47 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1905 helix: 1.88 (0.20), residues: 715 sheet: -1.91 (0.23), residues: 430 loop : -1.59 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.002 0.000 HIS B 119 PHE 0.024 0.001 PHE A 233 TYR 0.024 0.002 TYR C 67 ARG 0.002 0.000 ARG D 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 15) link_NAG-ASN : angle 1.07757 ( 45) link_BETA1-4 : bond 0.00310 ( 10) link_BETA1-4 : angle 1.07640 ( 30) hydrogen bonds : bond 0.03600 ( 695) hydrogen bonds : angle 4.65516 ( 2190) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.65663 ( 10) covalent geometry : bond 0.00270 (16545) covalent geometry : angle 0.57332 (22610) *********************** 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 171 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 1.634 Fit side-chains REVERT: A 180 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8599 (pp) REVERT: A 262 TYR cc_start: 0.7809 (t80) cc_final: 0.7548 (t80) REVERT: A 315 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7334 (mtt90) REVERT: E 129 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8748 (pp) REVERT: E 262 TYR cc_start: 0.7839 (t80) cc_final: 0.7551 (t80) REVERT: E 291 MET cc_start: 0.7156 (ttp) cc_final: 0.6807 (ttm) REVERT: E 315 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7248 (mtt90) REVERT: B 315 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7311 (mtt180) REVERT: B 428 ARG cc_start: 0.6393 (mpt180) cc_final: 0.6103 (tpt170) REVERT: B 459 TRP cc_start: 0.5112 (m-10) cc_final: 0.4807 (m-10) REVERT: C 262 TYR cc_start: 0.7852 (t80) cc_final: 0.7575 (t80) REVERT: C 315 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7193 (mtt180) REVERT: C 428 ARG cc_start: 0.6210 (mpt180) cc_final: 0.5386 (mmt-90) REVERT: D 262 TYR cc_start: 0.7810 (t80) cc_final: 0.7556 (t80) REVERT: D 459 TRP cc_start: 0.6037 (OUTLIER) cc_final: 0.5663 (m-10) outliers start: 47 outliers final: 27 residues processed: 158 average time/residue: 0.2687 time to fit residues: 63.5164 Evaluate side-chains 140 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 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 B residue 30 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 315 ARG 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 260 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 16 optimal weight: 0.0370 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.085493 restraints weight = 26268.543| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.07 r_work: 0.2932 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16575 Z= 0.134 Angle : 0.588 9.022 22695 Z= 0.288 Chirality : 0.044 0.146 2680 Planarity : 0.004 0.026 2755 Dihedral : 6.046 83.089 2645 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.95 % Allowed : 14.22 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1905 helix: 2.06 (0.20), residues: 715 sheet: -1.91 (0.23), residues: 430 loop : -1.50 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 156 HIS 0.002 0.000 HIS D 119 PHE 0.024 0.002 PHE A 254 TYR 0.025 0.002 TYR E 448 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 15) link_NAG-ASN : angle 1.12155 ( 45) link_BETA1-4 : bond 0.00269 ( 10) link_BETA1-4 : angle 1.20942 ( 30) hydrogen bonds : bond 0.03523 ( 695) hydrogen bonds : angle 4.57592 ( 2190) SS BOND : bond 0.00328 ( 5) SS BOND : angle 0.65524 ( 10) covalent geometry : bond 0.00314 (16545) covalent geometry : angle 0.58511 (22610) *********************** 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 160 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 109 time to evaluate : 1.807 Fit side-chains revert: symmetry clash REVERT: A 180 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8641 (pp) REVERT: A 262 TYR cc_start: 0.7788 (t80) cc_final: 0.7567 (t80) REVERT: A 315 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7320 (mtt90) REVERT: E 129 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8791 (pp) REVERT: E 262 TYR cc_start: 0.7898 (t80) cc_final: 0.7582 (t80) REVERT: E 291 MET cc_start: 0.7166 (ttp) cc_final: 0.6831 (ttm) REVERT: E 315 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7286 (mtt90) REVERT: B 315 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7277 (mtt180) REVERT: B 428 ARG cc_start: 0.6405 (mpt180) cc_final: 0.5640 (mmt-90) REVERT: B 459 TRP cc_start: 0.5116 (m-10) cc_final: 0.4789 (m-10) REVERT: C 291 MET cc_start: 0.7105 (ttp) cc_final: 0.6803 (ttt) REVERT: C 315 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7116 (mtt180) REVERT: C 428 ARG cc_start: 0.6218 (mpt180) cc_final: 0.5403 (mmt-90) REVERT: D 459 TRP cc_start: 0.6058 (OUTLIER) cc_final: 0.5682 (m-10) outliers start: 51 outliers final: 33 residues processed: 147 average time/residue: 0.2925 time to fit residues: 64.5051 Evaluate side-chains 146 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 180 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG 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 167 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 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 289 VAL 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 C residue 59 THR 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 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 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 65 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.083623 restraints weight = 26110.576| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.04 r_work: 0.2897 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16575 Z= 0.186 Angle : 0.627 9.034 22695 Z= 0.308 Chirality : 0.046 0.158 2680 Planarity : 0.004 0.029 2755 Dihedral : 6.018 84.525 2645 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.12 % Allowed : 14.45 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1905 helix: 2.12 (0.20), residues: 715 sheet: -1.92 (0.23), residues: 430 loop : -1.42 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.004 0.001 HIS D 119 PHE 0.032 0.002 PHE C 233 TYR 0.026 0.002 TYR E 448 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 15) link_NAG-ASN : angle 1.23141 ( 45) link_BETA1-4 : bond 0.00271 ( 10) link_BETA1-4 : angle 1.29981 ( 30) hydrogen bonds : bond 0.03731 ( 695) hydrogen bonds : angle 4.63824 ( 2190) SS BOND : bond 0.00395 ( 5) SS BOND : angle 0.69228 ( 10) covalent geometry : bond 0.00450 (16545) covalent geometry : angle 0.62407 (22610) *********************** 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 159 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8605 (pp) REVERT: A 315 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7397 (mtt90) REVERT: E 129 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8813 (pp) REVERT: E 262 TYR cc_start: 0.7918 (t80) cc_final: 0.7597 (t80) REVERT: E 291 MET cc_start: 0.7219 (ttp) cc_final: 0.6916 (ttm) REVERT: E 315 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7280 (mtt90) REVERT: B 291 MET cc_start: 0.7196 (ttp) cc_final: 0.6967 (ttt) REVERT: B 315 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7286 (mtt180) REVERT: B 428 ARG cc_start: 0.6407 (mpt180) cc_final: 0.5966 (tpt170) REVERT: B 459 TRP cc_start: 0.5158 (m-10) cc_final: 0.4834 (m-10) REVERT: C 291 MET cc_start: 0.6952 (ttp) cc_final: 0.6622 (ttt) REVERT: C 315 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7131 (mtt180) REVERT: C 428 ARG cc_start: 0.6379 (mpt180) cc_final: 0.5632 (mmt-90) REVERT: D 459 TRP cc_start: 0.6155 (OUTLIER) cc_final: 0.5766 (m-10) outliers start: 54 outliers final: 40 residues processed: 148 average time/residue: 0.2933 time to fit residues: 65.0588 Evaluate side-chains 148 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 180 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 409 ILE 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 167 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 429 VAL Chi-restraints excluded: chain E residue 443 LEU 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 289 VAL 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 C residue 59 THR 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 129 LEU 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 225 VAL Chi-restraints excluded: chain D residue 260 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 167 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.084418 restraints weight = 26355.252| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.17 r_work: 0.2918 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4001 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= 0.129 Angle : 0.582 8.317 22695 Z= 0.287 Chirality : 0.044 0.143 2680 Planarity : 0.004 0.027 2755 Dihedral : 5.669 82.917 2645 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1905 helix: 2.27 (0.20), residues: 715 sheet: -1.87 (0.23), residues: 430 loop : -1.37 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.002 0.000 HIS B 119 PHE 0.032 0.002 PHE C 233 TYR 0.024 0.002 TYR E 448 ARG 0.002 0.000 ARG C 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 15) link_NAG-ASN : angle 1.15098 ( 45) link_BETA1-4 : bond 0.00290 ( 10) link_BETA1-4 : angle 1.14936 ( 30) hydrogen bonds : bond 0.03436 ( 695) hydrogen bonds : angle 4.49873 ( 2190) SS BOND : bond 0.00291 ( 5) SS BOND : angle 0.59370 ( 10) covalent geometry : bond 0.00302 (16545) covalent geometry : angle 0.57910 (22610) *********************** 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 171 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 315 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7389 (mtt90) REVERT: E 105 ASP cc_start: 0.8336 (p0) cc_final: 0.8005 (p0) REVERT: E 129 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8777 (pp) REVERT: E 262 TYR cc_start: 0.7908 (t80) cc_final: 0.7610 (t80) REVERT: E 291 MET cc_start: 0.7232 (ttp) cc_final: 0.6948 (ttm) REVERT: E 315 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7277 (mtt90) REVERT: B 315 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7305 (mtt180) REVERT: B 428 ARG cc_start: 0.6385 (mpt180) cc_final: 0.5660 (mmt-90) REVERT: B 459 TRP cc_start: 0.5195 (m-10) cc_final: 0.4897 (m-10) REVERT: C 291 MET cc_start: 0.6970 (ttp) cc_final: 0.6647 (ttt) REVERT: C 315 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7147 (mtt180) REVERT: C 428 ARG cc_start: 0.6336 (mpt180) cc_final: 0.5590 (mmt-90) REVERT: D 459 TRP cc_start: 0.6162 (OUTLIER) cc_final: 0.5790 (m-10) outliers start: 47 outliers final: 36 residues processed: 159 average time/residue: 0.2884 time to fit residues: 68.5416 Evaluate side-chains 154 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 180 ILE 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 429 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 229 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 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 C residue 59 THR 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 D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR 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 229 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 101 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 131 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.086344 restraints weight = 26295.096| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.09 r_work: 0.2947 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16575 Z= 0.106 Angle : 0.575 8.169 22695 Z= 0.281 Chirality : 0.043 0.138 2680 Planarity : 0.004 0.026 2755 Dihedral : 5.261 78.139 2645 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.49 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1905 helix: 2.41 (0.20), residues: 715 sheet: -1.85 (0.23), residues: 430 loop : -1.33 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 156 HIS 0.002 0.000 HIS B 158 PHE 0.033 0.002 PHE B 233 TYR 0.023 0.002 TYR E 448 ARG 0.005 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 15) link_NAG-ASN : angle 1.09991 ( 45) link_BETA1-4 : bond 0.00339 ( 10) link_BETA1-4 : angle 1.13346 ( 30) hydrogen bonds : bond 0.03160 ( 695) hydrogen bonds : angle 4.39500 ( 2190) SS BOND : bond 0.00247 ( 5) SS BOND : angle 0.56569 ( 10) covalent geometry : bond 0.00240 (16545) covalent geometry : angle 0.57286 (22610) ********************** 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 164 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7285 (mtt90) REVERT: E 129 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8745 (pp) REVERT: E 262 TYR cc_start: 0.7912 (t80) cc_final: 0.7596 (t80) REVERT: E 291 MET cc_start: 0.7275 (ttp) cc_final: 0.6937 (ttm) REVERT: E 315 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7266 (mtt90) REVERT: E 428 ARG cc_start: 0.6825 (mpt180) cc_final: 0.6145 (mmt180) REVERT: B 291 MET cc_start: 0.7081 (ttp) cc_final: 0.6840 (ttt) REVERT: B 315 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7277 (mtt180) REVERT: B 428 ARG cc_start: 0.6274 (mpt180) cc_final: 0.5609 (mmt-90) REVERT: B 459 TRP cc_start: 0.5170 (m-10) cc_final: 0.4874 (m-10) REVERT: C 291 MET cc_start: 0.6709 (ttp) cc_final: 0.6368 (ttt) REVERT: C 315 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7072 (mtt180) REVERT: C 428 ARG cc_start: 0.6271 (mpt180) cc_final: 0.5511 (mmt-90) REVERT: D 459 TRP cc_start: 0.6205 (OUTLIER) cc_final: 0.5738 (m-10) outliers start: 43 outliers final: 35 residues processed: 154 average time/residue: 0.2747 time to fit residues: 63.7947 Evaluate side-chains 153 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 229 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 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 C residue 59 THR 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 D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR 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 229 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 85 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 77 optimal weight: 0.0040 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.087741 restraints weight = 25960.818| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.08 r_work: 0.2969 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16575 Z= 0.103 Angle : 0.563 7.519 22695 Z= 0.277 Chirality : 0.043 0.241 2680 Planarity : 0.004 0.026 2755 Dihedral : 4.891 70.544 2645 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.31 % Allowed : 15.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1905 helix: 2.58 (0.20), residues: 710 sheet: -2.08 (0.22), residues: 450 loop : -1.08 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 156 HIS 0.001 0.000 HIS B 460 PHE 0.030 0.002 PHE A 233 TYR 0.023 0.002 TYR E 448 ARG 0.002 0.000 ARG A 428 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 15) link_NAG-ASN : angle 1.06575 ( 45) link_BETA1-4 : bond 0.00308 ( 10) link_BETA1-4 : angle 1.10122 ( 30) hydrogen bonds : bond 0.03026 ( 695) hydrogen bonds : angle 4.30438 ( 2190) SS BOND : bond 0.00235 ( 5) SS BOND : angle 0.58471 ( 10) covalent geometry : bond 0.00231 (16545) covalent geometry : angle 0.56027 (22610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8995.53 seconds wall clock time: 156 minutes 32.17 seconds (9392.17 seconds total)