Starting phenix.real_space_refine on Sun Aug 24 01:59:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hiq_0227/08_2025/6hiq_0227.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hiq_0227/08_2025/6hiq_0227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hiq_0227/08_2025/6hiq_0227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hiq_0227/08_2025/6hiq_0227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hiq_0227/08_2025/6hiq_0227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hiq_0227/08_2025/6hiq_0227.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10580 2.51 5 N 2595 2.21 5 O 2890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16110 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3139 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 3.59, per 1000 atoms: 0.22 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: 1.12 Conformation dependent library (CDL) restraints added in 446.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 44.4% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 176' Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY A 249 " --> pdb=" O PRO A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.863A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 460 removed outlier: 3.561A pdb=" N VAL A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU E 15 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.601A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 176' Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 241 removed outlier: 3.503A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL E 237 " --> pdb=" O PHE E 233 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY E 249 " --> pdb=" O PRO E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 268 " --> pdb=" O VAL E 264 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU E 294 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 332 removed outlier: 3.862A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU E 405 " --> pdb=" O GLY E 401 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 436 " --> pdb=" O VAL E 432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 437 " --> pdb=" O LEU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 460 removed outlier: 3.562A pdb=" N VAL E 453 " --> pdb=" O SER E 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.627A pdb=" N LEU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 176' Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 245 through 249 removed outlier: 4.186A pdb=" N GLY B 249 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.863A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 460 removed outlier: 3.562A pdb=" N VAL B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 176' Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 237 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY C 249 " --> pdb=" O PRO C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 268 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 269 " --> pdb=" O PHE C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 294 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 removed outlier: 3.862A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 447 removed outlier: 3.979A pdb=" N GLU C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 460 removed outlier: 3.561A pdb=" N VAL C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 removed outlier: 3.628A pdb=" N LEU D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.600A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 170 through 176' Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.504A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 237 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 245 through 249 removed outlier: 4.187A pdb=" N GLY D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 3.588A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.647A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU D 294 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.863A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 447 removed outlier: 3.980A pdb=" N GLU D 405 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 436 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 437 " --> pdb=" O LEU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 460 removed outlier: 3.561A pdb=" N VAL D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 65 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 164 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG E 65 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN E 164 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 65 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 164 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.620A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG C 65 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 164 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.128A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.128A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.621A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 65 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN D 164 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.127A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.39 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 16575 Z= 0.300 Angle : 1.084 12.097 22695 Z= 0.529 Chirality : 0.061 0.277 2680 Planarity : 0.006 0.055 2755 Dihedral : 10.850 87.130 6300 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.29 % Allowed : 4.91 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.97 (0.14), residues: 1905 helix: -4.19 (0.09), residues: 685 sheet: -2.40 (0.22), residues: 405 loop : -2.76 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 217 TYR 0.037 0.004 TYR B 116 PHE 0.016 0.002 PHE D 287 TRP 0.044 0.003 TRP B 168 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00687 (16545) covalent geometry : angle 1.08188 (22610) SS BOND : bond 0.00330 ( 5) SS BOND : angle 0.32285 ( 10) hydrogen bonds : bond 0.30332 ( 695) hydrogen bonds : angle 10.21342 ( 2190) link_BETA1-4 : bond 0.00634 ( 10) link_BETA1-4 : angle 1.66798 ( 30) link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.77108 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 0.359 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: 0.1493 time to fit residues: 56.0197 Evaluate side-chains 137 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D 158 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.124908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.088583 restraints weight = 26387.539| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.06 r_work: 0.2998 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16575 Z= 0.166 Angle : 0.702 7.657 22695 Z= 0.349 Chirality : 0.047 0.162 2680 Planarity : 0.005 0.039 2755 Dihedral : 8.627 86.755 2645 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 9.19 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.18), residues: 1905 helix: -1.53 (0.16), residues: 715 sheet: -2.22 (0.21), residues: 475 loop : -1.94 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 410 TYR 0.028 0.002 TYR E 67 PHE 0.023 0.002 PHE D 233 TRP 0.022 0.002 TRP E 168 HIS 0.005 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00371 (16545) covalent geometry : angle 0.70022 (22610) SS BOND : bond 0.00305 ( 5) SS BOND : angle 0.33278 ( 10) hydrogen bonds : bond 0.05947 ( 695) hydrogen bonds : angle 6.00800 ( 2190) link_BETA1-4 : bond 0.00210 ( 10) link_BETA1-4 : angle 1.23067 ( 30) link_NAG-ASN : bond 0.00143 ( 15) link_NAG-ASN : angle 1.12952 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.9065 (tpp) cc_final: 0.8798 (tpp) REVERT: A 262 TYR cc_start: 0.7752 (t80) cc_final: 0.7383 (t80) REVERT: E 262 TYR cc_start: 0.7662 (t80) cc_final: 0.7420 (t80) REVERT: E 291 MET cc_start: 0.7178 (ttp) cc_final: 0.6950 (ttm) REVERT: E 415 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7782 (mmtm) REVERT: E 419 MET cc_start: 0.8259 (mmm) cc_final: 0.7480 (tmm) REVERT: B 250 GLU cc_start: 0.7598 (tt0) cc_final: 0.7375 (tt0) REVERT: B 262 TYR cc_start: 0.7707 (t80) cc_final: 0.7287 (t80) REVERT: B 291 MET cc_start: 0.7596 (ttp) cc_final: 0.7357 (ttp) REVERT: C 233 PHE cc_start: 0.7990 (t80) cc_final: 0.7741 (t80) REVERT: D 105 ASP cc_start: 0.8073 (p0) cc_final: 0.7862 (p0) REVERT: D 262 TYR cc_start: 0.7770 (t80) cc_final: 0.7503 (t80) REVERT: D 291 MET cc_start: 0.7642 (ttp) cc_final: 0.7259 (ttp) REVERT: D 410 ARG cc_start: 0.7850 (ptm-80) cc_final: 0.7187 (tmm160) REVERT: D 415 LYS cc_start: 0.7929 (ttmt) cc_final: 0.7435 (mmtm) REVERT: D 418 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7970 (tp30) REVERT: D 419 MET cc_start: 0.7928 (mmm) cc_final: 0.7280 (tmm) outliers start: 43 outliers final: 17 residues processed: 205 average time/residue: 0.1117 time to fit residues: 33.6879 Evaluate side-chains 135 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 459 TRP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 187 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.087119 restraints weight = 26657.185| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.12 r_work: 0.2966 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16575 Z= 0.153 Angle : 0.640 8.626 22695 Z= 0.314 Chirality : 0.045 0.169 2680 Planarity : 0.004 0.032 2755 Dihedral : 7.809 87.767 2645 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.18 % Allowed : 10.81 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.19), residues: 1905 helix: 0.18 (0.19), residues: 720 sheet: -2.10 (0.22), residues: 455 loop : -1.71 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 439 TYR 0.027 0.002 TYR B 67 PHE 0.024 0.002 PHE E 254 TRP 0.018 0.001 TRP D 168 HIS 0.004 0.001 HIS A 460 Details of bonding type rmsd covalent geometry : bond 0.00348 (16545) covalent geometry : angle 0.63735 (22610) SS BOND : bond 0.00448 ( 5) SS BOND : angle 0.80756 ( 10) hydrogen bonds : bond 0.04698 ( 695) hydrogen bonds : angle 5.15088 ( 2190) link_BETA1-4 : bond 0.00348 ( 10) link_BETA1-4 : angle 1.21963 ( 30) link_NAG-ASN : bond 0.00138 ( 15) link_NAG-ASN : angle 1.20251 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7778 (t80) cc_final: 0.7455 (t80) REVERT: A 315 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7331 (mtt90) REVERT: E 262 TYR cc_start: 0.7593 (t80) cc_final: 0.7365 (t80) REVERT: E 418 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7854 (tp30) REVERT: E 419 MET cc_start: 0.8202 (mmm) cc_final: 0.7324 (tmm) REVERT: B 262 TYR cc_start: 0.7655 (t80) cc_final: 0.7276 (t80) REVERT: B 315 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7338 (mtt180) REVERT: B 428 ARG cc_start: 0.6697 (mpt180) cc_final: 0.6192 (tpt170) REVERT: B 459 TRP cc_start: 0.5812 (OUTLIER) cc_final: 0.5574 (m-10) REVERT: C 233 PHE cc_start: 0.8119 (t80) cc_final: 0.7759 (t80) REVERT: C 262 TYR cc_start: 0.7767 (t80) cc_final: 0.7462 (t80) REVERT: D 262 TYR cc_start: 0.7684 (t80) cc_final: 0.7436 (t80) REVERT: D 291 MET cc_start: 0.7595 (ttp) cc_final: 0.7167 (ttp) REVERT: D 298 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7925 (tp) REVERT: D 418 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7705 (tp30) REVERT: D 419 MET cc_start: 0.8009 (mmm) cc_final: 0.7468 (tmm) REVERT: D 424 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7086 (tmm-80) REVERT: D 459 TRP cc_start: 0.5972 (OUTLIER) cc_final: 0.5411 (m-10) outliers start: 55 outliers final: 19 residues processed: 169 average time/residue: 0.1057 time to fit residues: 26.9176 Evaluate side-chains 138 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 TRP 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 106 VAL 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 228 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 103 optimal weight: 0.0670 chunk 2 optimal weight: 0.1980 chunk 97 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.124574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089497 restraints weight = 26454.853| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.17 r_work: 0.2978 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16575 Z= 0.111 Angle : 0.576 7.012 22695 Z= 0.286 Chirality : 0.043 0.144 2680 Planarity : 0.004 0.030 2755 Dihedral : 7.037 85.293 2645 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.89 % Allowed : 12.37 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.20), residues: 1905 helix: 1.10 (0.19), residues: 715 sheet: -2.02 (0.22), residues: 455 loop : -1.58 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 439 TYR 0.023 0.001 TYR A 67 PHE 0.025 0.001 PHE E 233 TRP 0.014 0.001 TRP D 168 HIS 0.001 0.000 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00241 (16545) covalent geometry : angle 0.57331 (22610) SS BOND : bond 0.00284 ( 5) SS BOND : angle 0.60372 ( 10) hydrogen bonds : bond 0.03833 ( 695) hydrogen bonds : angle 4.86696 ( 2190) link_BETA1-4 : bond 0.00351 ( 10) link_BETA1-4 : angle 1.08844 ( 30) link_NAG-ASN : bond 0.00184 ( 15) link_NAG-ASN : angle 1.01489 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7800 (t80) cc_final: 0.7449 (t80) REVERT: A 291 MET cc_start: 0.7561 (ttm) cc_final: 0.7268 (ttp) REVERT: A 315 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7368 (mtt90) REVERT: E 129 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8644 (pp) REVERT: E 262 TYR cc_start: 0.7593 (t80) cc_final: 0.7353 (t80) REVERT: E 418 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7877 (tp30) REVERT: E 419 MET cc_start: 0.8110 (mmm) cc_final: 0.7214 (tmm) REVERT: E 428 ARG cc_start: 0.6641 (mpt180) cc_final: 0.6235 (tpt170) REVERT: B 105 ASP cc_start: 0.8167 (p0) cc_final: 0.7965 (p0) REVERT: B 215 ILE cc_start: 0.8898 (pt) cc_final: 0.8662 (pt) REVERT: B 262 TYR cc_start: 0.7541 (t80) cc_final: 0.7269 (t80) REVERT: B 291 MET cc_start: 0.7204 (ttp) cc_final: 0.6871 (ttp) REVERT: B 315 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7248 (mtt180) REVERT: B 428 ARG cc_start: 0.6426 (mpt180) cc_final: 0.5944 (tpt170) REVERT: C 129 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8849 (pp) REVERT: C 233 PHE cc_start: 0.8068 (t80) cc_final: 0.7669 (t80) REVERT: C 315 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7362 (mtt90) REVERT: C 428 ARG cc_start: 0.6276 (mpt180) cc_final: 0.5409 (mmt-90) REVERT: D 262 TYR cc_start: 0.7717 (t80) cc_final: 0.7432 (t80) REVERT: D 291 MET cc_start: 0.7638 (ttp) cc_final: 0.7165 (ttp) REVERT: D 298 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8002 (tp) REVERT: D 418 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7701 (tp30) REVERT: D 419 MET cc_start: 0.8060 (mmm) cc_final: 0.7482 (tmm) REVERT: D 459 TRP cc_start: 0.5989 (OUTLIER) cc_final: 0.5483 (m-10) outliers start: 50 outliers final: 17 residues processed: 179 average time/residue: 0.1070 time to fit residues: 29.2532 Evaluate side-chains 138 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 273 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 100 ILE 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 D residue 24 LYS Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 118 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 177 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 171 optimal weight: 0.4980 chunk 134 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 178 optimal weight: 0.0470 chunk 31 optimal weight: 7.9990 overall best weight: 0.4680 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.125233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.090446 restraints weight = 26527.041| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.16 r_work: 0.2990 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16575 Z= 0.103 Angle : 0.565 10.055 22695 Z= 0.276 Chirality : 0.043 0.159 2680 Planarity : 0.003 0.026 2755 Dihedral : 6.282 80.895 2645 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.01 % Allowed : 12.60 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.20), residues: 1905 helix: 1.70 (0.20), residues: 710 sheet: -1.93 (0.22), residues: 455 loop : -1.45 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 439 TYR 0.022 0.001 TYR D 67 PHE 0.024 0.001 PHE C 254 TRP 0.010 0.001 TRP C 168 HIS 0.001 0.000 HIS C 460 Details of bonding type rmsd covalent geometry : bond 0.00224 (16545) covalent geometry : angle 0.56272 (22610) SS BOND : bond 0.00286 ( 5) SS BOND : angle 0.67508 ( 10) hydrogen bonds : bond 0.03471 ( 695) hydrogen bonds : angle 4.67460 ( 2190) link_BETA1-4 : bond 0.00287 ( 10) link_BETA1-4 : angle 1.08439 ( 30) link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 1.06966 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.8225 (t80) cc_final: 0.7957 (t80) REVERT: A 262 TYR cc_start: 0.7813 (t80) cc_final: 0.7490 (t80) REVERT: A 291 MET cc_start: 0.7638 (ttm) cc_final: 0.7407 (ttp) REVERT: A 315 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7394 (mtt90) REVERT: E 262 TYR cc_start: 0.7739 (t80) cc_final: 0.7457 (t80) REVERT: E 418 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8037 (tp30) REVERT: E 419 MET cc_start: 0.8115 (mmm) cc_final: 0.7290 (tmm) REVERT: B 129 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8849 (pp) REVERT: B 215 ILE cc_start: 0.8858 (pt) cc_final: 0.8626 (pt) REVERT: B 262 TYR cc_start: 0.7500 (t80) cc_final: 0.7217 (t80) REVERT: B 291 MET cc_start: 0.7209 (ttp) cc_final: 0.6887 (ttp) REVERT: B 315 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7240 (mtt180) REVERT: B 428 ARG cc_start: 0.6338 (mpt180) cc_final: 0.6094 (tpt170) REVERT: C 129 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8831 (pp) REVERT: C 233 PHE cc_start: 0.8090 (t80) cc_final: 0.7881 (t80) REVERT: C 315 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7334 (mtt180) REVERT: C 428 ARG cc_start: 0.6360 (mpt180) cc_final: 0.5963 (mmt-90) REVERT: D 262 TYR cc_start: 0.7739 (t80) cc_final: 0.7487 (t80) REVERT: D 291 MET cc_start: 0.7700 (ttp) cc_final: 0.7191 (ttp) REVERT: D 298 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7936 (tp) REVERT: D 418 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7930 (tp30) REVERT: D 419 MET cc_start: 0.8132 (mmm) cc_final: 0.7506 (tmm) REVERT: D 459 TRP cc_start: 0.5994 (OUTLIER) cc_final: 0.5530 (m-10) outliers start: 52 outliers final: 27 residues processed: 177 average time/residue: 0.1121 time to fit residues: 29.9340 Evaluate side-chains 149 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 129 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 100 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 65 optimal weight: 0.0170 overall best weight: 0.5836 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.125224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088625 restraints weight = 26247.519| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.10 r_work: 0.2996 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16575 Z= 0.103 Angle : 0.558 8.727 22695 Z= 0.274 Chirality : 0.043 0.143 2680 Planarity : 0.003 0.025 2755 Dihedral : 5.764 75.346 2645 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.83 % Allowed : 13.12 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.20), residues: 1905 helix: 2.00 (0.20), residues: 715 sheet: -1.89 (0.22), residues: 455 loop : -1.40 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 439 TYR 0.022 0.001 TYR A 67 PHE 0.024 0.001 PHE E 254 TRP 0.010 0.001 TRP C 168 HIS 0.001 0.000 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00229 (16545) covalent geometry : angle 0.55572 (22610) SS BOND : bond 0.00265 ( 5) SS BOND : angle 0.62603 ( 10) hydrogen bonds : bond 0.03296 ( 695) hydrogen bonds : angle 4.56330 ( 2190) link_BETA1-4 : bond 0.00307 ( 10) link_BETA1-4 : angle 1.09817 ( 30) link_NAG-ASN : bond 0.00141 ( 15) link_NAG-ASN : angle 1.03008 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.8220 (t80) cc_final: 0.7921 (t80) REVERT: A 262 TYR cc_start: 0.7804 (t80) cc_final: 0.7489 (t80) REVERT: A 291 MET cc_start: 0.7644 (ttm) cc_final: 0.7424 (ttp) REVERT: A 315 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7404 (mtt90) REVERT: E 129 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8758 (pp) REVERT: E 262 TYR cc_start: 0.7763 (t80) cc_final: 0.7520 (t80) REVERT: B 129 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8820 (pp) REVERT: B 215 ILE cc_start: 0.8821 (pt) cc_final: 0.8606 (pt) REVERT: B 262 TYR cc_start: 0.7577 (t80) cc_final: 0.7341 (t80) REVERT: B 291 MET cc_start: 0.7285 (ttp) cc_final: 0.6928 (ttp) REVERT: B 315 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7271 (mtt180) REVERT: B 428 ARG cc_start: 0.6375 (mpt180) cc_final: 0.5694 (mmt-90) REVERT: C 129 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8806 (pp) REVERT: C 233 PHE cc_start: 0.8185 (t80) cc_final: 0.7896 (t80) REVERT: C 315 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7253 (mtt180) REVERT: C 428 ARG cc_start: 0.6342 (mpt180) cc_final: 0.5964 (mmt-90) REVERT: D 235 MET cc_start: 0.7833 (mmt) cc_final: 0.7624 (mmp) REVERT: D 262 TYR cc_start: 0.7714 (t80) cc_final: 0.7504 (t80) REVERT: D 291 MET cc_start: 0.7699 (ttp) cc_final: 0.7168 (ttp) REVERT: D 298 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7928 (tp) REVERT: D 419 MET cc_start: 0.8107 (mmm) cc_final: 0.7678 (tmm) REVERT: D 459 TRP cc_start: 0.6056 (OUTLIER) cc_final: 0.5599 (m-10) outliers start: 49 outliers final: 33 residues processed: 162 average time/residue: 0.1112 time to fit residues: 27.1996 Evaluate side-chains 150 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 273 LEU 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 30 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 115 optimal weight: 0.0270 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 120 optimal weight: 0.0970 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.085113 restraints weight = 26303.236| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.16 r_work: 0.2930 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16575 Z= 0.147 Angle : 0.596 8.418 22695 Z= 0.294 Chirality : 0.045 0.161 2680 Planarity : 0.004 0.029 2755 Dihedral : 5.681 71.182 2645 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.47 % Allowed : 12.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1905 helix: 2.23 (0.20), residues: 715 sheet: -1.82 (0.23), residues: 430 loop : -1.45 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.023 0.002 TYR E 448 PHE 0.026 0.002 PHE D 233 TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00351 (16545) covalent geometry : angle 0.59305 (22610) SS BOND : bond 0.00354 ( 5) SS BOND : angle 0.69880 ( 10) hydrogen bonds : bond 0.03518 ( 695) hydrogen bonds : angle 4.57023 ( 2190) link_BETA1-4 : bond 0.00227 ( 10) link_BETA1-4 : angle 1.23188 ( 30) link_NAG-ASN : bond 0.00136 ( 15) link_NAG-ASN : angle 1.19673 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7815 (t80) cc_final: 0.7588 (t80) REVERT: A 291 MET cc_start: 0.7730 (ttm) cc_final: 0.7510 (ttp) REVERT: A 315 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7283 (mtt90) REVERT: E 105 ASP cc_start: 0.8389 (p0) cc_final: 0.8087 (p0) REVERT: E 129 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8705 (pp) REVERT: E 262 TYR cc_start: 0.7792 (t80) cc_final: 0.7584 (t80) REVERT: E 315 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7263 (mtt90) REVERT: B 129 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8927 (pp) REVERT: B 215 ILE cc_start: 0.8877 (pt) cc_final: 0.8654 (pt) REVERT: B 262 TYR cc_start: 0.7639 (t80) cc_final: 0.7367 (t80) REVERT: B 315 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7317 (mtt180) REVERT: B 428 ARG cc_start: 0.6527 (mpt180) cc_final: 0.5918 (mmt-90) REVERT: C 129 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8936 (pp) REVERT: C 233 PHE cc_start: 0.8194 (t80) cc_final: 0.7905 (t80) REVERT: C 315 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7142 (mtt180) REVERT: C 428 ARG cc_start: 0.6218 (mpt180) cc_final: 0.5436 (mmt-90) REVERT: D 180 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8622 (pp) REVERT: D 262 TYR cc_start: 0.7892 (t80) cc_final: 0.7632 (t80) REVERT: D 291 MET cc_start: 0.7820 (ttp) cc_final: 0.7264 (ttp) REVERT: D 298 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7839 (tp) REVERT: D 419 MET cc_start: 0.8302 (mmm) cc_final: 0.7636 (tmm) REVERT: D 459 TRP cc_start: 0.6053 (OUTLIER) cc_final: 0.5680 (m-10) outliers start: 60 outliers final: 42 residues processed: 161 average time/residue: 0.1154 time to fit residues: 27.8050 Evaluate side-chains 157 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 VAL 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 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 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 180 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 229 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 187 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 142 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.122028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.084612 restraints weight = 26254.914| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.18 r_work: 0.2923 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16575 Z= 0.149 Angle : 0.587 8.930 22695 Z= 0.289 Chirality : 0.044 0.149 2680 Planarity : 0.004 0.030 2755 Dihedral : 5.541 67.445 2645 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.06 % Allowed : 13.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.20), residues: 1905 helix: 2.34 (0.20), residues: 715 sheet: -1.85 (0.23), residues: 430 loop : -1.38 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.024 0.002 TYR E 448 PHE 0.025 0.002 PHE D 233 TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00359 (16545) covalent geometry : angle 0.58376 (22610) SS BOND : bond 0.00346 ( 5) SS BOND : angle 0.63168 ( 10) hydrogen bonds : bond 0.03485 ( 695) hydrogen bonds : angle 4.53603 ( 2190) link_BETA1-4 : bond 0.00271 ( 10) link_BETA1-4 : angle 1.19602 ( 30) link_NAG-ASN : bond 0.00136 ( 15) link_NAG-ASN : angle 1.15357 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7808 (t80) cc_final: 0.7583 (t80) REVERT: A 291 MET cc_start: 0.7693 (ttm) cc_final: 0.7487 (ttp) REVERT: A 315 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7312 (mtt90) REVERT: E 105 ASP cc_start: 0.8389 (p0) cc_final: 0.8091 (p0) REVERT: E 129 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8810 (pp) REVERT: E 262 TYR cc_start: 0.7856 (t80) cc_final: 0.7602 (t80) REVERT: E 315 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7244 (mtt90) REVERT: B 129 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8893 (pp) REVERT: B 215 ILE cc_start: 0.8923 (pt) cc_final: 0.8713 (pt) REVERT: B 262 TYR cc_start: 0.7617 (t80) cc_final: 0.7294 (t80) REVERT: B 291 MET cc_start: 0.7422 (ttp) cc_final: 0.7161 (ttp) REVERT: B 315 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7325 (mtt180) REVERT: B 428 ARG cc_start: 0.6433 (mpt180) cc_final: 0.5805 (mmt-90) REVERT: C 129 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8929 (pp) REVERT: C 233 PHE cc_start: 0.8207 (t80) cc_final: 0.7936 (t80) REVERT: C 315 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7133 (mtt180) REVERT: C 428 ARG cc_start: 0.6267 (mpt180) cc_final: 0.5484 (mmt-90) REVERT: D 180 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8611 (pp) REVERT: D 291 MET cc_start: 0.7780 (ttp) cc_final: 0.7196 (ttp) REVERT: D 459 TRP cc_start: 0.6015 (OUTLIER) cc_final: 0.5657 (m-10) outliers start: 53 outliers final: 41 residues processed: 152 average time/residue: 0.1199 time to fit residues: 27.2651 Evaluate side-chains 152 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 289 VAL 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 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 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 180 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 229 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 151 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 181 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.122551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.086712 restraints weight = 26141.546| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.06 r_work: 0.2950 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16575 Z= 0.119 Angle : 0.565 8.394 22695 Z= 0.278 Chirality : 0.043 0.139 2680 Planarity : 0.004 0.029 2755 Dihedral : 5.162 57.323 2645 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.54 % Allowed : 14.05 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.20), residues: 1905 helix: 2.50 (0.20), residues: 710 sheet: -1.84 (0.22), residues: 430 loop : -1.29 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.024 0.002 TYR E 448 PHE 0.030 0.001 PHE A 233 TRP 0.011 0.001 TRP B 156 HIS 0.002 0.000 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00277 (16545) covalent geometry : angle 0.56262 (22610) SS BOND : bond 0.00288 ( 5) SS BOND : angle 0.60537 ( 10) hydrogen bonds : bond 0.03268 ( 695) hydrogen bonds : angle 4.44003 ( 2190) link_BETA1-4 : bond 0.00296 ( 10) link_BETA1-4 : angle 1.13860 ( 30) link_NAG-ASN : bond 0.00140 ( 15) link_NAG-ASN : angle 1.12984 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7790 (t80) cc_final: 0.7525 (t80) REVERT: A 315 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7255 (mtt90) REVERT: E 105 ASP cc_start: 0.8354 (p0) cc_final: 0.8086 (p0) REVERT: E 129 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8748 (pp) REVERT: E 262 TYR cc_start: 0.7863 (t80) cc_final: 0.7606 (t80) REVERT: E 315 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7254 (mtt90) REVERT: E 428 ARG cc_start: 0.6587 (mpt180) cc_final: 0.5912 (mmt-90) REVERT: B 129 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8862 (pp) REVERT: B 215 ILE cc_start: 0.8914 (pt) cc_final: 0.8694 (pt) REVERT: B 262 TYR cc_start: 0.7587 (t80) cc_final: 0.7248 (t80) REVERT: B 291 MET cc_start: 0.7289 (ttp) cc_final: 0.7003 (ttp) REVERT: B 315 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7320 (mtt180) REVERT: B 428 ARG cc_start: 0.6441 (mpt180) cc_final: 0.5807 (mmt-90) REVERT: C 129 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8875 (pp) REVERT: C 315 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7049 (mtt180) REVERT: C 428 ARG cc_start: 0.6235 (mpt180) cc_final: 0.5460 (mmt-90) REVERT: D 24 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8732 (mttt) REVERT: D 459 TRP cc_start: 0.6069 (OUTLIER) cc_final: 0.5696 (m-10) outliers start: 44 outliers final: 32 residues processed: 151 average time/residue: 0.1237 time to fit residues: 27.2147 Evaluate side-chains 149 residues out of total 1800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 315 ARG Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 315 ARG Chi-restraints excluded: chain D residue 424 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 459 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6357 > 50: distance: 57 - 60: 16.759 distance: 60 - 61: 22.914 distance: 61 - 62: 7.044 distance: 61 - 64: 13.784 distance: 62 - 63: 18.744 distance: 62 - 68: 18.830 distance: 64 - 65: 42.523 distance: 64 - 66: 18.547 distance: 65 - 67: 31.295 distance: 68 - 69: 21.743 distance: 69 - 70: 28.071 distance: 70 - 71: 39.247 distance: 70 - 72: 56.291 distance: 72 - 73: 3.126 distance: 73 - 74: 31.919 distance: 73 - 76: 5.056 distance: 74 - 75: 4.940 distance: 74 - 79: 17.283 distance: 76 - 77: 31.435 distance: 76 - 78: 34.427 distance: 79 - 80: 24.297 distance: 79 - 85: 12.197 distance: 80 - 81: 21.607 distance: 80 - 83: 20.894 distance: 81 - 82: 16.755 distance: 81 - 86: 27.913 distance: 82 - 106: 24.097 distance: 83 - 84: 20.468 distance: 84 - 85: 35.512 distance: 86 - 87: 12.590 distance: 87 - 88: 13.415 distance: 87 - 90: 13.767 distance: 88 - 89: 18.969 distance: 88 - 94: 4.407 distance: 90 - 91: 11.222 distance: 91 - 92: 28.960 distance: 91 - 93: 23.909 distance: 94 - 95: 9.003 distance: 95 - 96: 6.023 distance: 95 - 98: 7.544 distance: 96 - 97: 15.352 distance: 96 - 102: 15.219 distance: 97 - 125: 37.304 distance: 98 - 99: 23.743 distance: 98 - 100: 30.949 distance: 99 - 101: 27.816 distance: 102 - 103: 24.338 distance: 103 - 104: 16.619 distance: 104 - 105: 32.364 distance: 104 - 106: 17.249 distance: 106 - 107: 15.085 distance: 107 - 108: 14.041 distance: 107 - 110: 22.282 distance: 108 - 109: 7.232 distance: 108 - 113: 21.585 distance: 109 - 143: 29.636 distance: 110 - 111: 12.263 distance: 110 - 112: 54.805 distance: 113 - 114: 5.769 distance: 114 - 115: 18.415 distance: 114 - 117: 11.403 distance: 115 - 116: 9.049 distance: 115 - 125: 12.542 distance: 116 - 150: 17.483 distance: 117 - 118: 19.953 distance: 118 - 119: 14.138 distance: 118 - 120: 9.379 distance: 119 - 121: 16.890 distance: 120 - 122: 11.085 distance: 121 - 123: 5.732 distance: 122 - 123: 11.234 distance: 123 - 124: 31.411 distance: 125 - 126: 4.806 distance: 126 - 127: 12.766 distance: 126 - 129: 4.566 distance: 127 - 128: 27.268 distance: 127 - 136: 5.556 distance: 128 - 156: 28.118 distance: 129 - 130: 11.715 distance: 130 - 131: 9.193 distance: 130 - 132: 8.260 distance: 131 - 133: 9.642 distance: 132 - 134: 6.671 distance: 133 - 135: 5.040 distance: 134 - 135: 12.428