Starting phenix.real_space_refine on Fri Sep 27 13:45:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/09_2024/6hiq_0227.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/09_2024/6hiq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/09_2024/6hiq_0227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/09_2024/6hiq_0227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/09_2024/6hiq_0227.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hiq_0227/09_2024/6hiq_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-5461/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: 10.04, per 1000 atoms: 0.62 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: 4.15 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: 1.98 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: 5.30 Time building geometry restraints manager: 4.87 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.160 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.170 ------------------------------------------------------------------------------- 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 16545 Z= 0.451 Angle : 1.082 12.097 22610 Z= 0.528 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 274 time to evaluate : 1.806 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: 0.3849 time to fit residues: 143.9351 Evaluate side-chains 137 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 16545 Z= 0.208 Angle : 0.695 8.342 22610 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 *********************** 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 fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7624 (t80) cc_final: 0.7308 (t80) REVERT: A 291 MET cc_start: 0.7093 (ttm) cc_final: 0.6767 (ttp) REVERT: E 250 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7056 (pt0) REVERT: E 286 TYR cc_start: 0.7781 (t80) cc_final: 0.7492 (t80) REVERT: E 415 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7804 (mmtm) REVERT: E 419 MET cc_start: 0.8107 (mmm) cc_final: 0.7512 (tmm) REVERT: B 262 TYR cc_start: 0.7493 (t80) cc_final: 0.7211 (t80) REVERT: C 233 PHE cc_start: 0.7859 (t80) cc_final: 0.7620 (t80) REVERT: D 286 TYR cc_start: 0.7924 (t80) cc_final: 0.7362 (t80) REVERT: D 291 MET cc_start: 0.7177 (ttp) cc_final: 0.6773 (ttp) REVERT: D 410 ARG cc_start: 0.7801 (ptm-80) cc_final: 0.7164 (tmm160) REVERT: D 415 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7559 (mmtm) REVERT: D 418 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7878 (tp30) REVERT: D 419 MET cc_start: 0.7780 (mmm) cc_final: 0.7242 (tmm) outliers start: 41 outliers final: 15 residues processed: 202 average time/residue: 0.2729 time to fit residues: 82.0825 Evaluate side-chains 132 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 B 460 HIS C 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16545 Z= 0.315 Angle : 0.684 8.218 22610 Z= 0.338 Chirality : 0.047 0.173 2680 Planarity : 0.004 0.032 2755 Dihedral : 8.130 88.791 2645 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.87 % Allowed : 10.69 % Favored : 85.43 % 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: -1.74 (0.19), residues: 1905 helix: 0.15 (0.19), residues: 720 sheet: -1.98 (0.22), residues: 475 loop : -1.75 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 168 HIS 0.006 0.001 HIS D 119 PHE 0.021 0.002 PHE D 233 TYR 0.026 0.002 TYR B 67 ARG 0.004 0.001 ARG A 169 *********************** 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 190 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 123 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7738 (t80) cc_final: 0.7457 (t80) REVERT: A 291 MET cc_start: 0.7240 (ttm) cc_final: 0.6982 (ttp) REVERT: A 315 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6939 (mtt90) REVERT: E 418 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7759 (tp30) REVERT: E 419 MET cc_start: 0.8112 (mmm) cc_final: 0.7338 (tmm) REVERT: B 315 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7253 (mtt180) REVERT: B 428 ARG cc_start: 0.6599 (mpt180) cc_final: 0.5993 (tpt170) REVERT: C 262 TYR cc_start: 0.7663 (t80) cc_final: 0.7415 (t80) REVERT: D 291 MET cc_start: 0.7080 (ttp) cc_final: 0.6699 (ttp) REVERT: D 418 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7659 (tp30) REVERT: D 419 MET cc_start: 0.7933 (mmm) cc_final: 0.7446 (tmm) REVERT: D 424 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7044 (tmm-80) outliers start: 67 outliers final: 27 residues processed: 180 average time/residue: 0.2790 time to fit residues: 75.3196 Evaluate side-chains 135 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16545 Z= 0.251 Angle : 0.622 7.747 22610 Z= 0.307 Chirality : 0.045 0.164 2680 Planarity : 0.004 0.030 2755 Dihedral : 7.530 88.060 2645 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.28 % Allowed : 12.02 % 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: -1.07 (0.20), residues: 1905 helix: 1.15 (0.20), residues: 715 sheet: -2.02 (0.22), residues: 430 loop : -1.66 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 168 HIS 0.004 0.001 HIS B 119 PHE 0.029 0.002 PHE C 233 TYR 0.026 0.002 TYR A 67 ARG 0.004 0.000 ARG E 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 122 time to evaluate : 1.824 Fit side-chains REVERT: A 262 TYR cc_start: 0.7731 (t80) cc_final: 0.7455 (t80) REVERT: A 315 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6914 (mtt90) REVERT: E 129 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8419 (pp) REVERT: E 418 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7898 (tp30) REVERT: B 315 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: B 428 ARG cc_start: 0.6406 (mpt180) cc_final: 0.5920 (tpt170) REVERT: C 129 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8674 (pp) REVERT: C 428 ARG cc_start: 0.6259 (mpt180) cc_final: 0.5442 (mmt-90) REVERT: D 250 GLU cc_start: 0.7405 (tt0) cc_final: 0.7200 (pt0) REVERT: D 418 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7643 (tp30) REVERT: D 419 MET cc_start: 0.8016 (mmm) cc_final: 0.7569 (tmm) outliers start: 74 outliers final: 38 residues processed: 187 average time/residue: 0.2619 time to fit residues: 75.0128 Evaluate side-chains 147 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 105 time to evaluate : 1.735 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 288 VAL 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 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 136 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 0.0040 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16545 Z= 0.162 Angle : 0.571 9.469 22610 Z= 0.282 Chirality : 0.043 0.151 2680 Planarity : 0.004 0.027 2755 Dihedral : 6.644 84.924 2645 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.95 % Allowed : 12.77 % Favored : 84.28 % 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: -0.69 (0.20), residues: 1905 helix: 1.68 (0.20), residues: 715 sheet: -1.95 (0.23), residues: 455 loop : -1.57 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.001 0.000 HIS D 119 PHE 0.026 0.001 PHE C 233 TYR 0.023 0.002 TYR A 67 ARG 0.002 0.000 ARG C 439 *********************** 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 185 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 2.033 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7687 (t80) cc_final: 0.7461 (t80) REVERT: A 315 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7001 (mtt90) REVERT: E 129 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8542 (pp) REVERT: E 315 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7109 (mtt90) REVERT: B 215 ILE cc_start: 0.8853 (pt) cc_final: 0.8648 (pt) REVERT: B 315 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: B 428 ARG cc_start: 0.6265 (mpt180) cc_final: 0.5475 (mmt-90) REVERT: C 129 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8597 (pp) REVERT: C 315 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7117 (mtt180) REVERT: C 428 ARG cc_start: 0.6114 (mpt180) cc_final: 0.5275 (mmt-90) REVERT: D 418 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7896 (tp30) REVERT: D 419 MET cc_start: 0.8086 (mmm) cc_final: 0.7542 (tmm) outliers start: 51 outliers final: 27 residues processed: 176 average time/residue: 0.2724 time to fit residues: 72.7626 Evaluate side-chains 143 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16545 Z= 0.272 Angle : 0.617 9.197 22610 Z= 0.303 Chirality : 0.045 0.160 2680 Planarity : 0.004 0.028 2755 Dihedral : 6.308 85.265 2645 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.53 % Allowed : 13.12 % Favored : 83.35 % 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: -0.48 (0.20), residues: 1905 helix: 1.94 (0.20), residues: 715 sheet: -1.81 (0.23), residues: 450 loop : -1.58 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.003 0.001 HIS E 119 PHE 0.024 0.002 PHE E 254 TYR 0.023 0.002 TYR E 448 ARG 0.004 0.000 ARG E 428 *********************** 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 168 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 107 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7748 (t80) cc_final: 0.7527 (t80) REVERT: A 315 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7061 (mtt90) REVERT: E 129 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8430 (pp) REVERT: E 315 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7132 (mtt90) REVERT: B 315 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: B 428 ARG cc_start: 0.6266 (mpt180) cc_final: 0.5859 (tpt170) REVERT: C 129 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8701 (pp) REVERT: C 428 ARG cc_start: 0.6232 (mpt180) cc_final: 0.5455 (mmt-90) outliers start: 61 outliers final: 45 residues processed: 160 average time/residue: 0.2991 time to fit residues: 72.1572 Evaluate side-chains 152 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 102 time to evaluate : 1.866 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 264 VAL 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 59 THR Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 289 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 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16545 Z= 0.345 Angle : 0.650 8.694 22610 Z= 0.322 Chirality : 0.047 0.158 2680 Planarity : 0.004 0.029 2755 Dihedral : 6.171 88.198 2645 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.70 % Allowed : 13.70 % Favored : 82.60 % 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: -0.33 (0.20), residues: 1905 helix: 2.05 (0.20), residues: 715 sheet: -1.81 (0.23), residues: 450 loop : -1.42 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 156 HIS 0.004 0.001 HIS D 119 PHE 0.031 0.002 PHE A 233 TYR 0.031 0.002 TYR E 61 ARG 0.004 0.000 ARG A 169 *********************** 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 171 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 107 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: A 315 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7132 (mtt90) REVERT: E 129 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8436 (pp) REVERT: E 315 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7122 (mtt90) REVERT: B 315 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7108 (mtt180) REVERT: B 428 ARG cc_start: 0.6216 (mpt180) cc_final: 0.5729 (tpt170) REVERT: C 428 ARG cc_start: 0.6384 (mpt180) cc_final: 0.5674 (mmt-90) outliers start: 64 outliers final: 53 residues processed: 164 average time/residue: 0.3151 time to fit residues: 79.1753 Evaluate side-chains 157 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 100 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 160 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 160 ILE 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 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 180 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 VAL 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 225 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 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 264 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 35 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16545 Z= 0.184 Angle : 0.581 7.364 22610 Z= 0.287 Chirality : 0.044 0.138 2680 Planarity : 0.004 0.027 2755 Dihedral : 5.575 86.453 2645 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.72 % Allowed : 14.86 % 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: -0.18 (0.20), residues: 1905 helix: 2.25 (0.20), residues: 715 sheet: -1.85 (0.23), residues: 430 loop : -1.36 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.002 0.000 HIS B 119 PHE 0.030 0.002 PHE A 233 TYR 0.024 0.002 TYR C 67 ARG 0.002 0.000 ARG E 428 *********************** 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 168 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7082 (mtt90) REVERT: E 105 ASP cc_start: 0.7854 (p0) cc_final: 0.7464 (p0) REVERT: E 129 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8537 (pp) REVERT: E 315 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7104 (mtt90) REVERT: E 428 ARG cc_start: 0.6594 (mpt180) cc_final: 0.5849 (mmt180) REVERT: B 315 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7099 (mtt180) REVERT: B 428 ARG cc_start: 0.6158 (mpt180) cc_final: 0.5453 (mmt-90) REVERT: C 428 ARG cc_start: 0.6227 (mpt180) cc_final: 0.5494 (mmt-90) outliers start: 47 outliers final: 34 residues processed: 160 average time/residue: 0.2801 time to fit residues: 67.3777 Evaluate side-chains 148 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 160 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 403 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 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 129 LEU Chi-restraints excluded: chain B residue 225 VAL 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 229 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 315 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 102 optimal weight: 0.0050 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16545 Z= 0.177 Angle : 0.574 7.524 22610 Z= 0.281 Chirality : 0.044 0.141 2680 Planarity : 0.004 0.027 2755 Dihedral : 5.252 83.400 2645 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.60 % Allowed : 15.03 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.20), residues: 1905 helix: 2.45 (0.20), residues: 710 sheet: -1.83 (0.23), residues: 430 loop : -1.25 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.001 0.000 HIS A 119 PHE 0.031 0.002 PHE A 233 TYR 0.021 0.002 TYR C 67 ARG 0.002 0.000 ARG E 428 *********************** 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 165 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.864 Fit side-chains REVERT: A 315 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7110 (mtt90) REVERT: E 105 ASP cc_start: 0.7850 (p0) cc_final: 0.7632 (p0) REVERT: E 129 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8542 (pp) REVERT: E 315 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7144 (mtt90) REVERT: E 428 ARG cc_start: 0.6557 (mpt180) cc_final: 0.5820 (mmt180) REVERT: B 22 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: B 291 MET cc_start: 0.6661 (ttp) cc_final: 0.6443 (ttt) REVERT: B 315 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7095 (mtt180) REVERT: B 428 ARG cc_start: 0.6152 (mpt180) cc_final: 0.5511 (mmt-90) REVERT: C 315 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7018 (mtt180) REVERT: C 428 ARG cc_start: 0.6199 (mpt180) cc_final: 0.5477 (mmt-90) outliers start: 45 outliers final: 36 residues processed: 155 average time/residue: 0.2830 time to fit residues: 66.1240 Evaluate side-chains 153 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 111 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 160 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 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 129 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 264 VAL 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 229 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16545 Z= 0.223 Angle : 0.600 9.179 22610 Z= 0.294 Chirality : 0.044 0.136 2680 Planarity : 0.004 0.028 2755 Dihedral : 5.253 82.423 2645 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.72 % Allowed : 14.97 % Favored : 82.31 % 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: 0.01 (0.20), residues: 1905 helix: 2.46 (0.20), residues: 710 sheet: -1.84 (0.23), residues: 430 loop : -1.21 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 459 HIS 0.002 0.001 HIS D 119 PHE 0.032 0.002 PHE C 233 TYR 0.024 0.002 TYR E 448 ARG 0.003 0.000 ARG A 428 ********************** 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 159 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 112 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7111 (mtt90) REVERT: E 105 ASP cc_start: 0.7871 (p0) cc_final: 0.7546 (p0) REVERT: E 129 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8483 (pp) REVERT: E 235 MET cc_start: 0.8810 (mmm) cc_final: 0.8511 (mmm) REVERT: E 315 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7154 (mtt90) REVERT: E 428 ARG cc_start: 0.6532 (mpt180) cc_final: 0.5807 (mmt180) REVERT: B 22 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7447 (m-40) REVERT: B 291 MET cc_start: 0.6677 (ttp) cc_final: 0.6439 (ttt) REVERT: B 315 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7093 (mtt180) REVERT: B 428 ARG cc_start: 0.6140 (mpt180) cc_final: 0.5527 (mmt-90) REVERT: C 315 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6948 (mtt180) REVERT: C 428 ARG cc_start: 0.6218 (mpt180) cc_final: 0.5511 (mmt-90) REVERT: D 262 TYR cc_start: 0.7876 (t80) cc_final: 0.7667 (t80) REVERT: D 291 MET cc_start: 0.7719 (tpp) cc_final: 0.7515 (tpp) outliers start: 47 outliers final: 39 residues processed: 149 average time/residue: 0.2853 time to fit residues: 64.1864 Evaluate side-chains 150 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 105 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 160 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 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 129 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 264 VAL 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 229 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.122261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.085362 restraints weight = 26436.437| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.16 r_work: 0.2934 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16545 Z= 0.165 Angle : 0.578 9.887 22610 Z= 0.283 Chirality : 0.044 0.204 2680 Planarity : 0.004 0.026 2755 Dihedral : 5.039 78.937 2645 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 15.26 % Favored : 82.25 % 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: 0.05 (0.20), residues: 1905 helix: 2.51 (0.20), residues: 710 sheet: -1.82 (0.23), residues: 430 loop : -1.20 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.002 0.000 HIS B 411 PHE 0.032 0.002 PHE A 233 TYR 0.021 0.002 TYR C 67 ARG 0.002 0.000 ARG D 218 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3132.60 seconds wall clock time: 56 minutes 52.72 seconds (3412.72 seconds total)