Starting phenix.real_space_refine on Fri May 16 11:00:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c54_16433/05_2025/8c54_16433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c54_16433/05_2025/8c54_16433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c54_16433/05_2025/8c54_16433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c54_16433/05_2025/8c54_16433.map" model { file = "/net/cci-nas-00/data/ceres_data/8c54_16433/05_2025/8c54_16433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c54_16433/05_2025/8c54_16433.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 72 5.16 5 C 8884 2.51 5 N 2404 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14266 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "B" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "C" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "D" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Time building chain proxies: 14.99, per 1000 atoms: 1.05 Number of scatterers: 14266 At special positions: 0 Unit cell: (97.4365, 103.464, 97.4365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 8 15.00 O 2898 8.00 N 2404 7.00 C 8884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 3.4 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 18 sheets defined 46.7% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 52 through 71 Processing helix chain 'A' and resid 74 through 92 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 107 through 129 removed outlier: 4.526A pdb=" N TYR A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.653A pdb=" N THR A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 172 " --> pdb=" O MET A 168 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.506A pdb=" N ILE A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 275 through 289 removed outlier: 3.674A pdb=" N ARG A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.725A pdb=" N VAL A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.761A pdb=" N LYS A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 74 through 92 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 107 through 129 removed outlier: 4.525A pdb=" N TYR B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.658A pdb=" N THR B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 172 " --> pdb=" O MET B 168 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 218 through 229 removed outlier: 3.507A pdb=" N ILE B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 251 Processing helix chain 'B' and resid 252 through 255 Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.673A pdb=" N ARG B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 357 removed outlier: 3.725A pdb=" N VAL B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.756A pdb=" N LYS B 390 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 428 through 439 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'C' and resid 11 through 15 Processing helix chain 'C' and resid 52 through 71 Processing helix chain 'C' and resid 74 through 92 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 129 removed outlier: 4.525A pdb=" N TYR C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 166 through 180 removed outlier: 3.660A pdb=" N THR C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 172 " --> pdb=" O MET C 168 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 218 through 229 removed outlier: 3.507A pdb=" N ILE C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 252 through 255 Processing helix chain 'C' and resid 275 through 289 removed outlier: 3.678A pdb=" N ARG C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 357 removed outlier: 3.724A pdb=" N VAL C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.756A pdb=" N LYS C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 Processing helix chain 'C' and resid 428 through 439 Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 52 through 71 Processing helix chain 'D' and resid 74 through 92 Processing helix chain 'D' and resid 92 through 105 Processing helix chain 'D' and resid 107 through 129 removed outlier: 4.525A pdb=" N TYR D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.659A pdb=" N THR D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 218 through 229 removed outlier: 3.507A pdb=" N ILE D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 252 through 255 Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.677A pdb=" N ARG D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 357 removed outlier: 3.726A pdb=" N VAL D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.772A pdb=" N LYS D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 414 Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 37 removed outlier: 5.641A pdb=" N ILE A 34 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN A 47 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 36 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.331A pdb=" N VAL C 378 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR C 377 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 400 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 379 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N SER C 402 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASN C 299 " --> pdb=" O PRO C 399 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE C 401 " --> pdb=" O ASN C 299 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE C 301 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE C 403 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 303 " --> pdb=" O PHE C 403 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 266 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TYR C 302 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 268 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLN C 304 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL C 270 " --> pdb=" O GLN C 304 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER C 422 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL C 444 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR A 483 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 446 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA A 485 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 146 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 146 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL D 444 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR B 483 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL D 446 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA B 485 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER D 422 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA D 266 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR D 302 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE D 268 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLN D 304 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 270 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASN D 299 " --> pdb=" O PRO D 399 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE D 401 " --> pdb=" O ASN D 299 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE D 301 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE D 403 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL D 303 " --> pdb=" O PHE D 403 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR D 377 " --> pdb=" O ALA D 398 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 400 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 379 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER D 402 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 378 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.526A pdb=" N VAL A 155 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR A 236 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA A 157 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR A 238 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 159 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.327A pdb=" N VAL A 378 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR A 377 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 400 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 379 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER A 402 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN A 299 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE A 401 " --> pdb=" O ASN A 299 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 301 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE A 403 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 303 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 266 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR A 302 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE A 268 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN A 304 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 270 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER A 422 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 146 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 146 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER B 422 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 266 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR B 302 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 268 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLN B 304 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL B 270 " --> pdb=" O GLN B 304 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN B 299 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE B 401 " --> pdb=" O ASN B 299 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 301 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 403 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 303 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 377 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE B 400 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 379 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER B 402 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 378 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 37 removed outlier: 5.657A pdb=" N ILE B 34 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 47 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 36 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.514A pdb=" N VAL B 155 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR B 236 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA B 157 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR B 238 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 159 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB2, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AB3, first strand: chain 'C' and resid 33 through 37 removed outlier: 5.642A pdb=" N ILE C 34 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN C 47 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 36 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 212 through 214 removed outlier: 6.523A pdb=" N VAL C 155 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR C 236 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 157 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR C 238 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 159 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 418 through 419 Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB7, first strand: chain 'D' and resid 33 through 37 removed outlier: 5.644A pdb=" N ILE D 34 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN D 47 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 36 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 212 through 214 removed outlier: 6.513A pdb=" N VAL D 155 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR D 236 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA D 157 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR D 238 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE D 159 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 418 through 419 726 hydrogen bonds defined for protein. 2042 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 4.15 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: 4600 1.34 - 1.46: 2015 1.46 - 1.57: 7473 1.57 - 1.69: 12 1.69 - 1.81: 124 Bond restraints: 14224 Sorted by residual: bond pdb=" O5B NAI D 501 " pdb=" PA NAI D 501 " ideal model delta sigma weight residual 1.644 1.569 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O5B NAI B 501 " pdb=" PA NAI B 501 " ideal model delta sigma weight residual 1.644 1.570 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O5B NAI A 501 " pdb=" PA NAI A 501 " ideal model delta sigma weight residual 1.644 1.570 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5B NAI C 501 " pdb=" PA NAI C 501 " ideal model delta sigma weight residual 1.644 1.571 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O5D NAI C 501 " pdb=" PN NAI C 501 " ideal model delta sigma weight residual 1.650 1.578 0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 14219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 19037 1.65 - 3.30: 324 3.30 - 4.94: 39 4.94 - 6.59: 4 6.59 - 8.24: 8 Bond angle restraints: 19412 Sorted by residual: angle pdb=" O1N NAI D 501 " pdb=" PN NAI D 501 " pdb=" O2N NAI D 501 " ideal model delta sigma weight residual 123.22 114.98 8.24 3.00e+00 1.11e-01 7.54e+00 angle pdb=" O1N NAI C 501 " pdb=" PN NAI C 501 " pdb=" O2N NAI C 501 " ideal model delta sigma weight residual 123.22 114.99 8.23 3.00e+00 1.11e-01 7.53e+00 angle pdb=" O1N NAI B 501 " pdb=" PN NAI B 501 " pdb=" O2N NAI B 501 " ideal model delta sigma weight residual 123.22 115.01 8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" O1N NAI A 501 " pdb=" PN NAI A 501 " pdb=" O2N NAI A 501 " ideal model delta sigma weight residual 123.22 115.01 8.21 3.00e+00 1.11e-01 7.48e+00 angle pdb=" PA NAI C 501 " pdb=" O3 NAI C 501 " pdb=" PN NAI C 501 " ideal model delta sigma weight residual 129.27 136.72 -7.45 3.00e+00 1.11e-01 6.17e+00 ... (remaining 19407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7447 17.86 - 35.73: 761 35.73 - 53.59: 236 53.59 - 71.45: 84 71.45 - 89.32: 56 Dihedral angle restraints: 8584 sinusoidal: 3128 harmonic: 5456 Sorted by residual: dihedral pdb=" CA ASN A 118 " pdb=" C ASN A 118 " pdb=" N ALA A 119 " pdb=" CA ALA A 119 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASN C 118 " pdb=" C ASN C 118 " pdb=" N ALA C 119 " pdb=" CA ALA C 119 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN B 118 " pdb=" C ASN B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1343 0.029 - 0.058: 576 0.058 - 0.087: 177 0.087 - 0.116: 150 0.116 - 0.146: 30 Chirality restraints: 2276 Sorted by residual: chirality pdb=" C2B NAI D 501 " pdb=" C1B NAI D 501 " pdb=" C3B NAI D 501 " pdb=" O2B NAI D 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C2B NAI A 501 " pdb=" C1B NAI A 501 " pdb=" C3B NAI A 501 " pdb=" O2B NAI A 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C2B NAI B 501 " pdb=" C1B NAI B 501 " pdb=" C3B NAI B 501 " pdb=" O2B NAI B 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2273 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 307 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C VAL A 307 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 307 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 308 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 307 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C VAL C 307 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL C 307 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 307 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C VAL D 307 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL D 307 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA D 308 " -0.008 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2644 2.77 - 3.30: 13685 3.30 - 3.83: 26919 3.83 - 4.37: 32596 4.37 - 4.90: 52840 Nonbonded interactions: 128684 Sorted by model distance: nonbonded pdb=" OH TYR A 473 " pdb=" OD2 ASP C 135 " model vdw 2.233 3.040 nonbonded pdb=" O CYS A 297 " pdb=" O HOH A 601 " model vdw 2.236 3.040 nonbonded pdb=" O CYS B 297 " pdb=" O HOH B 601 " model vdw 2.236 3.040 nonbonded pdb=" O CYS C 297 " pdb=" O HOH C 601 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP A 135 " pdb=" OH TYR C 473 " model vdw 2.237 3.040 ... (remaining 128679 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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=0.00 max=1.00 mean=0.99 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: 0.850 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 42.960 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.004 0.075 14224 Z= 0.208 Angle : 0.559 8.240 19412 Z= 0.279 Chirality : 0.043 0.146 2276 Planarity : 0.004 0.024 2500 Dihedral : 18.809 89.318 5112 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.43 % Allowed : 20.48 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1936 helix: 1.19 (0.19), residues: 792 sheet: -0.22 (0.25), residues: 376 loop : 0.09 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 70 HIS 0.002 0.000 HIS D 349 PHE 0.018 0.002 PHE A 125 TYR 0.008 0.001 TYR C 483 ARG 0.002 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.13174 ( 726) hydrogen bonds : angle 6.36858 ( 2042) covalent geometry : bond 0.00441 (14224) covalent geometry : angle 0.55903 (19412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.441 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 164 average time/residue: 1.0709 time to fit residues: 196.0251 Evaluate side-chains 164 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 163 ASN C 163 ASN D 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121489 restraints weight = 47564.418| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.54 r_work: 0.3097 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14224 Z= 0.262 Angle : 0.625 4.835 19412 Z= 0.336 Chirality : 0.046 0.145 2276 Planarity : 0.005 0.032 2500 Dihedral : 9.509 82.134 2352 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.36 % Allowed : 19.16 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1936 helix: 0.83 (0.18), residues: 796 sheet: -0.15 (0.26), residues: 372 loop : 0.08 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 70 HIS 0.002 0.001 HIS B 349 PHE 0.021 0.003 PHE A 125 TYR 0.009 0.002 TYR B 483 ARG 0.004 0.001 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.06085 ( 726) hydrogen bonds : angle 5.46831 ( 2042) covalent geometry : bond 0.00598 (14224) covalent geometry : angle 0.62519 (19412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 1.571 Fit side-chains REVERT: A 394 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: B 394 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: C 394 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: C 483 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.7014 (t80) REVERT: D 394 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: D 483 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7044 (t80) outliers start: 48 outliers final: 25 residues processed: 169 average time/residue: 1.1701 time to fit residues: 218.9766 Evaluate side-chains 159 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 483 TYR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 483 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 145 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS D 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.144463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123306 restraints weight = 52238.163| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.43 r_work: 0.3151 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14224 Z= 0.131 Angle : 0.482 4.513 19412 Z= 0.259 Chirality : 0.042 0.136 2276 Planarity : 0.004 0.024 2500 Dihedral : 8.160 86.882 2328 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.41 % Allowed : 20.48 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1936 helix: 1.27 (0.19), residues: 796 sheet: -0.10 (0.26), residues: 372 loop : 0.22 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 70 HIS 0.001 0.000 HIS C 349 PHE 0.017 0.002 PHE B 125 TYR 0.005 0.001 TYR A 473 ARG 0.001 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 726) hydrogen bonds : angle 5.00491 ( 2042) covalent geometry : bond 0.00282 (14224) covalent geometry : angle 0.48231 (19412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.450 Fit side-chains REVERT: A 127 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8182 (mt-10) REVERT: A 394 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: B 394 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: C 127 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 394 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: D 394 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6445 (m-80) outliers start: 23 outliers final: 12 residues processed: 153 average time/residue: 1.1684 time to fit residues: 199.7115 Evaluate side-chains 142 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119389 restraints weight = 51996.829| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.37 r_work: 0.3096 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14224 Z= 0.282 Angle : 0.633 4.931 19412 Z= 0.342 Chirality : 0.047 0.147 2276 Planarity : 0.005 0.034 2500 Dihedral : 8.523 80.940 2320 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.96 % Allowed : 19.63 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.18), residues: 1936 helix: 0.78 (0.18), residues: 800 sheet: -0.14 (0.26), residues: 372 loop : -0.04 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 70 HIS 0.003 0.001 HIS C 349 PHE 0.022 0.003 PHE B 424 TYR 0.010 0.002 TYR C 483 ARG 0.005 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.06132 ( 726) hydrogen bonds : angle 5.41162 ( 2042) covalent geometry : bond 0.00646 (14224) covalent geometry : angle 0.63258 (19412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.410 Fit side-chains REVERT: A 394 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: B 394 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: C 128 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8506 (mm-30) REVERT: C 394 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: C 483 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.7131 (t80) REVERT: D 394 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: D 483 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.7132 (t80) outliers start: 30 outliers final: 23 residues processed: 142 average time/residue: 1.2184 time to fit residues: 191.1373 Evaluate side-chains 149 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 483 TYR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 483 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.143225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122912 restraints weight = 45735.016| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.20 r_work: 0.3151 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14224 Z= 0.157 Angle : 0.510 4.473 19412 Z= 0.273 Chirality : 0.042 0.137 2276 Planarity : 0.004 0.023 2500 Dihedral : 8.172 83.704 2320 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.34 % Allowed : 19.70 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1936 helix: 1.17 (0.19), residues: 796 sheet: -0.13 (0.26), residues: 372 loop : 0.19 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 70 HIS 0.001 0.000 HIS C 349 PHE 0.018 0.002 PHE B 125 TYR 0.006 0.001 TYR C 483 ARG 0.002 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 726) hydrogen bonds : angle 5.08256 ( 2042) covalent geometry : bond 0.00345 (14224) covalent geometry : angle 0.50974 (19412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.783 Fit side-chains REVERT: A 312 THR cc_start: 0.7126 (t) cc_final: 0.6895 (m) REVERT: A 394 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: B 394 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: C 127 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8310 (mt-10) REVERT: C 394 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: D 394 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6516 (m-80) outliers start: 22 outliers final: 12 residues processed: 145 average time/residue: 1.1815 time to fit residues: 189.9038 Evaluate side-chains 138 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121294 restraints weight = 39871.905| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.73 r_work: 0.3147 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14224 Z= 0.176 Angle : 0.528 4.473 19412 Z= 0.283 Chirality : 0.043 0.139 2276 Planarity : 0.004 0.024 2500 Dihedral : 8.192 82.812 2320 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.80 % Allowed : 19.47 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.19), residues: 1936 helix: 1.15 (0.19), residues: 796 sheet: -0.11 (0.26), residues: 372 loop : 0.18 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 70 HIS 0.001 0.000 HIS C 349 PHE 0.019 0.002 PHE B 125 TYR 0.007 0.002 TYR C 483 ARG 0.003 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 726) hydrogen bonds : angle 5.12038 ( 2042) covalent geometry : bond 0.00391 (14224) covalent geometry : angle 0.52817 (19412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.492 Fit side-chains REVERT: A 312 THR cc_start: 0.7110 (t) cc_final: 0.6866 (m) REVERT: A 394 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: B 394 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: C 394 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: D 394 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: D 483 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.7150 (t80) outliers start: 28 outliers final: 16 residues processed: 146 average time/residue: 1.1412 time to fit residues: 185.0445 Evaluate side-chains 144 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 483 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 0.0870 chunk 189 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 142 optimal weight: 0.0970 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS B 349 HIS C 349 HIS D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128976 restraints weight = 51598.945| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.42 r_work: 0.3220 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14224 Z= 0.089 Angle : 0.429 4.429 19412 Z= 0.229 Chirality : 0.041 0.131 2276 Planarity : 0.003 0.028 2500 Dihedral : 7.697 87.526 2320 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.87 % Allowed : 19.78 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 1936 helix: 1.85 (0.19), residues: 780 sheet: -0.36 (0.24), residues: 424 loop : 0.67 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 70 HIS 0.001 0.000 HIS D 405 PHE 0.014 0.001 PHE C 125 TYR 0.005 0.001 TYR A 86 ARG 0.002 0.000 ARG C 434 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 726) hydrogen bonds : angle 4.62605 ( 2042) covalent geometry : bond 0.00182 (14224) covalent geometry : angle 0.42896 (19412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.417 Fit side-chains REVERT: A 312 THR cc_start: 0.7077 (t) cc_final: 0.6834 (m) REVERT: A 394 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: B 312 THR cc_start: 0.7091 (t) cc_final: 0.6809 (m) REVERT: B 394 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: C 312 THR cc_start: 0.7095 (t) cc_final: 0.6811 (m) REVERT: C 394 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.6353 (m-80) REVERT: D 312 THR cc_start: 0.7086 (t) cc_final: 0.6804 (m) REVERT: D 394 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.6413 (m-80) outliers start: 16 outliers final: 12 residues processed: 171 average time/residue: 1.1176 time to fit residues: 213.6759 Evaluate side-chains 154 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 111 optimal weight: 0.3980 chunk 158 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.141379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120207 restraints weight = 38690.179| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.61 r_work: 0.3149 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14224 Z= 0.256 Angle : 0.605 4.988 19412 Z= 0.325 Chirality : 0.046 0.145 2276 Planarity : 0.005 0.031 2500 Dihedral : 8.151 81.204 2316 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.49 % Allowed : 20.25 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1936 helix: 1.04 (0.18), residues: 800 sheet: -0.16 (0.26), residues: 372 loop : 0.13 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 70 HIS 0.002 0.001 HIS A 349 PHE 0.021 0.003 PHE A 125 TYR 0.012 0.002 TYR D 483 ARG 0.004 0.001 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.05789 ( 726) hydrogen bonds : angle 5.28642 ( 2042) covalent geometry : bond 0.00583 (14224) covalent geometry : angle 0.60528 (19412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.458 Fit side-chains REVERT: A 394 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6540 (m-80) REVERT: B 394 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: C 394 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: D 394 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.6537 (m-80) outliers start: 24 outliers final: 20 residues processed: 147 average time/residue: 1.1850 time to fit residues: 192.8022 Evaluate side-chains 149 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 402 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 80 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN B 407 ASN C 407 ASN D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.143460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122879 restraints weight = 50219.790| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.38 r_work: 0.3137 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14224 Z= 0.170 Angle : 0.523 4.495 19412 Z= 0.280 Chirality : 0.043 0.139 2276 Planarity : 0.004 0.024 2500 Dihedral : 8.017 83.846 2316 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.18 % Allowed : 20.33 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 1936 helix: 1.18 (0.19), residues: 796 sheet: -0.15 (0.26), residues: 372 loop : 0.26 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 70 HIS 0.001 0.000 HIS C 349 PHE 0.018 0.002 PHE A 125 TYR 0.009 0.002 TYR C 473 ARG 0.003 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 726) hydrogen bonds : angle 5.12098 ( 2042) covalent geometry : bond 0.00375 (14224) covalent geometry : angle 0.52294 (19412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.488 Fit side-chains REVERT: A 312 THR cc_start: 0.7141 (t) cc_final: 0.6907 (m) REVERT: A 394 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: B 394 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: C 394 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: C 483 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.7053 (t80) REVERT: D 394 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6506 (m-80) outliers start: 20 outliers final: 15 residues processed: 143 average time/residue: 1.1736 time to fit residues: 186.0624 Evaluate side-chains 146 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain C residue 483 TYR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 402 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 13 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.144858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.124461 restraints weight = 47767.495| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.23 r_work: 0.3165 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14224 Z= 0.131 Angle : 0.482 4.507 19412 Z= 0.258 Chirality : 0.042 0.136 2276 Planarity : 0.004 0.026 2500 Dihedral : 7.899 86.113 2316 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.18 % Allowed : 20.33 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1936 helix: 1.38 (0.19), residues: 796 sheet: -0.13 (0.26), residues: 372 loop : 0.35 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 70 HIS 0.001 0.000 HIS D 349 PHE 0.017 0.002 PHE A 125 TYR 0.006 0.001 TYR D 473 ARG 0.002 0.000 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04400 ( 726) hydrogen bonds : angle 4.95624 ( 2042) covalent geometry : bond 0.00281 (14224) covalent geometry : angle 0.48165 (19412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.561 Fit side-chains REVERT: A 312 THR cc_start: 0.7101 (t) cc_final: 0.6877 (m) REVERT: A 394 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: B 312 THR cc_start: 0.7123 (t) cc_final: 0.6878 (m) REVERT: B 394 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: C 312 THR cc_start: 0.7117 (t) cc_final: 0.6873 (m) REVERT: C 394 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: D 312 THR cc_start: 0.7119 (t) cc_final: 0.6874 (m) REVERT: D 394 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.6491 (m-80) outliers start: 20 outliers final: 12 residues processed: 144 average time/residue: 1.2769 time to fit residues: 204.3282 Evaluate side-chains 142 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 402 SER Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 402 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 166 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.145629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.125172 restraints weight = 51744.541| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.54 r_work: 0.3158 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14224 Z= 0.123 Angle : 0.471 4.504 19412 Z= 0.252 Chirality : 0.042 0.137 2276 Planarity : 0.004 0.026 2500 Dihedral : 7.853 87.828 2316 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.64 % Allowed : 20.87 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1936 helix: 1.43 (0.19), residues: 800 sheet: -0.12 (0.26), residues: 372 loop : 0.45 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 70 HIS 0.001 0.000 HIS D 349 PHE 0.017 0.002 PHE D 125 TYR 0.006 0.001 TYR B 473 ARG 0.001 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 726) hydrogen bonds : angle 4.88223 ( 2042) covalent geometry : bond 0.00262 (14224) covalent geometry : angle 0.47098 (19412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9171.25 seconds wall clock time: 158 minutes 43.23 seconds (9523.23 seconds total)