Starting phenix.real_space_refine on Fri Jul 3 13:21:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c54_16433/07_2026/8c54_16433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c54_16433/07_2026/8c54_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_16433/07_2026/8c54_16433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c54_16433/07_2026/8c54_16433.map" model { file = "/net/cci-nas-00/data/ceres_data/8c54_16433/07_2026/8c54_16433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c54_16433/07_2026/8c54_16433.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c54_16433/07_2026/8c54_16433.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c54_16433/07_2026/8c54_16433.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'GLU:plan': 14, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} 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: 4.58, per 1000 atoms: 0.32 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: 1.08 Conformation dependent library (CDL) restraints added in 958.2 milliseconds 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: 0.38 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: 1.93 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 7387 17.86 - 35.73: 692 35.73 - 53.59: 225 53.59 - 71.45: 36 71.45 - 89.32: 44 Dihedral angle restraints: 8384 sinusoidal: 2928 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 8381 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.950 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 17.352 89.318 4912 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (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 ARG 0.002 0.000 ARG B 231 TYR 0.008 0.001 TYR C 483 PHE 0.018 0.002 PHE A 125 TRP 0.016 0.002 TRP C 70 HIS 0.002 0.000 HIS D 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.21 (14224) covalent geometry : angle 0.55903 / 0.28 (19412) hydrogen bonds : bond 0.13174 / 8.82 ( 726) hydrogen bonds : angle 6.36858 / 4.66 ( 2042) *********************** 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 : 0.505 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 164 average time/residue: 0.4522 time to fit residues: 82.8690 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 : 0.443 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3537 r_free = 0.3537 target = 0.140947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120026 restraints weight = 43388.144| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.86 r_work: 0.3130 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 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 = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14224 Z= 0.272 Angle : 0.630 4.551 19412 Z= 0.340 Chirality : 0.047 0.146 2276 Planarity : 0.005 0.034 2500 Dihedral : 7.204 51.202 2152 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.67 % Allowed : 18.77 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1936 helix: 0.81 (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 ARG 0.004 0.001 ARG A 231 TYR 0.010 0.002 TYR A 483 PHE 0.022 0.003 PHE B 424 TRP 0.022 0.003 TRP C 70 HIS 0.002 0.001 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 (14224) covalent geometry : angle 0.63016 / 0.34 (19412) hydrogen bonds : bond 0.06178 / 4.18 ( 726) hydrogen bonds : angle 5.49802 / 4.01 ( 2042) *********************** 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 185 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.519 Fit side-chains REVERT: A 394 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: B 394 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: C 394 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: C 483 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7119 (t80) REVERT: D 394 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: D 483 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.7132 (t80) outliers start: 52 outliers final: 28 residues processed: 173 average time/residue: 0.4780 time to fit residues: 91.9498 Evaluate side-chains 161 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 16 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 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 16 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 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 16 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 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 75 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.143520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123149 restraints weight = 46859.422| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.20 r_work: 0.3140 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 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 = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14224 Z= 0.190 Angle : 0.547 4.487 19412 Z= 0.294 Chirality : 0.044 0.140 2276 Planarity : 0.004 0.025 2500 Dihedral : 6.607 51.497 2128 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.96 % Allowed : 19.16 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1936 helix: 0.99 (0.19), residues: 796 sheet: -0.14 (0.26), residues: 372 loop : 0.11 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 231 TYR 0.007 0.002 TYR C 483 PHE 0.019 0.002 PHE D 125 TRP 0.018 0.002 TRP C 70 HIS 0.001 0.001 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (14224) covalent geometry : angle 0.54715 / 0.29 (19412) hydrogen bonds : bond 0.05232 / 3.55 ( 726) hydrogen bonds : angle 5.24186 / 3.83 ( 2042) *********************** 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 160 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.539 Fit side-chains REVERT: A 394 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: B 394 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: C 394 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: C 483 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.6945 (t80) REVERT: D 394 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: D 483 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.6957 (t80) outliers start: 30 outliers final: 20 residues processed: 156 average time/residue: 0.4704 time to fit residues: 81.6434 Evaluate side-chains 150 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 VAL 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 307 VAL 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 307 VAL 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 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 483 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 166 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 167 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3611 r_free = 0.3611 target = 0.147053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126612 restraints weight = 53635.903| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.55 r_work: 0.3177 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14224 Z= 0.102 Angle : 0.445 4.511 19412 Z= 0.238 Chirality : 0.041 0.134 2276 Planarity : 0.003 0.026 2500 Dihedral : 6.011 50.389 2124 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.34 % Allowed : 20.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 1936 helix: 1.47 (0.19), residues: 800 sheet: -0.27 (0.25), residues: 400 loop : 0.37 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 434 TYR 0.004 0.001 TYR B 86 PHE 0.015 0.001 PHE C 125 TRP 0.015 0.002 TRP A 70 HIS 0.001 0.000 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (14224) covalent geometry : angle 0.44499 / 0.24 (19412) hydrogen bonds : bond 0.03843 / 2.63 ( 726) hydrogen bonds : angle 4.78514 / 3.49 ( 2042) *********************** 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 164 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.520 Fit side-chains REVERT: A 394 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: B 127 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8035 (mt-10) REVERT: B 394 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: C 127 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 312 THR cc_start: 0.7118 (t) cc_final: 0.6833 (m) REVERT: C 394 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: D 312 THR cc_start: 0.7119 (t) cc_final: 0.6838 (m) REVERT: D 394 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.6413 (m-80) outliers start: 22 outliers final: 16 residues processed: 160 average time/residue: 0.4627 time to fit residues: 82.3687 Evaluate side-chains 154 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU 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 185 LEU 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 185 LEU 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 185 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 170 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3611 r_free = 0.3611 target = 0.147070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126592 restraints weight = 54265.260| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.60 r_work: 0.3174 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 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 = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14224 Z= 0.105 Angle : 0.442 4.544 19412 Z= 0.237 Chirality : 0.041 0.136 2276 Planarity : 0.003 0.027 2500 Dihedral : 5.838 48.914 2120 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.65 % Allowed : 20.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.19), residues: 1936 helix: 1.58 (0.19), residues: 800 sheet: -0.31 (0.24), residues: 424 loop : 0.48 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 131 TYR 0.004 0.001 TYR C 473 PHE 0.015 0.001 PHE C 125 TRP 0.014 0.002 TRP A 70 HIS 0.001 0.000 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (14224) covalent geometry : angle 0.44246 / 0.24 (19412) hydrogen bonds : bond 0.03900 / 2.66 ( 726) hydrogen bonds : angle 4.73915 / 3.46 ( 2042) *********************** 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 172 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.549 Fit side-chains REVERT: A 118 ASN cc_start: 0.7951 (m-40) cc_final: 0.7729 (m-40) REVERT: A 312 THR cc_start: 0.7115 (t) cc_final: 0.6834 (m) REVERT: A 394 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.6408 (m-80) REVERT: B 118 ASN cc_start: 0.7949 (m-40) cc_final: 0.7722 (m-40) REVERT: B 127 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8099 (mt-10) REVERT: B 312 THR cc_start: 0.7124 (t) cc_final: 0.6839 (m) REVERT: B 394 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: C 118 ASN cc_start: 0.7946 (m-40) cc_final: 0.7722 (m-40) REVERT: C 127 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8063 (mt-10) REVERT: C 394 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: D 118 ASN cc_start: 0.7941 (m-40) cc_final: 0.7714 (m-40) REVERT: D 394 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6423 (m-80) outliers start: 26 outliers final: 20 residues processed: 163 average time/residue: 0.5229 time to fit residues: 94.7742 Evaluate side-chains 168 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU 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 A residue 402 SER Chi-restraints excluded: chain B residue 185 LEU 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 185 LEU 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 C residue 402 SER Chi-restraints excluded: chain D residue 185 LEU 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 Chi-restraints excluded: chain D residue 402 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 183 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 83 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN B 163 ASN D 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.143635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124215 restraints weight = 42087.645| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.97 r_work: 0.3166 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 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 = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0765 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= 0.171 Angle : 0.517 4.540 19412 Z= 0.278 Chirality : 0.043 0.142 2276 Planarity : 0.004 0.025 2500 Dihedral : 6.154 48.747 2120 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.41 % Allowed : 20.64 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.19), residues: 1936 helix: 1.32 (0.19), residues: 796 sheet: -0.10 (0.26), residues: 372 loop : 0.33 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 231 TYR 0.007 0.002 TYR C 483 PHE 0.018 0.002 PHE A 125 TRP 0.017 0.002 TRP B 70 HIS 0.001 0.000 HIS B 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (14224) covalent geometry : angle 0.51733 / 0.28 (19412) hydrogen bonds : bond 0.04926 / 3.34 ( 726) hydrogen bonds : angle 5.06249 / 3.69 ( 2042) *********************** 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 155 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.666 Fit side-chains REVERT: A 128 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8371 (mm-30) REVERT: A 394 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: B 128 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8370 (mm-30) REVERT: B 394 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: C 128 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8365 (mm-30) REVERT: C 394 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: D 128 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8354 (mm-30) REVERT: D 394 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6483 (m-80) outliers start: 23 outliers final: 18 residues processed: 149 average time/residue: 0.5359 time to fit residues: 88.5541 Evaluate side-chains 150 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 402 SER 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 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 402 SER 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 Chi-restraints excluded: chain D residue 402 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3531 r_free = 0.3531 target = 0.140381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119234 restraints weight = 48011.769| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.27 r_work: 0.3096 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 14224 Z= 0.333 Angle : 0.688 5.370 19412 Z= 0.371 Chirality : 0.050 0.155 2276 Planarity : 0.006 0.042 2500 Dihedral : 6.760 50.888 2120 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.66 % Allowed : 18.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 1936 helix: 0.69 (0.18), residues: 796 sheet: -0.22 (0.26), residues: 392 loop : 0.24 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 231 TYR 0.013 0.003 TYR D 483 PHE 0.023 0.004 PHE A 424 TRP 0.021 0.004 TRP C 70 HIS 0.004 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.33 (14224) covalent geometry : angle 0.68751 / 0.37 (19412) hydrogen bonds : bond 0.06540 / 4.43 ( 726) hydrogen bonds : angle 5.48823 / 4.00 ( 2042) *********************** 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 167 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.399 Fit side-chains REVERT: A 128 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8521 (mm-30) REVERT: A 394 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6498 (m-80) REVERT: B 128 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8533 (mm-30) REVERT: B 394 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: C 128 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8504 (mm-30) REVERT: C 394 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6481 (m-80) REVERT: C 483 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7227 (t80) REVERT: D 128 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8502 (mm-30) REVERT: D 394 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: D 483 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7234 (t80) outliers start: 39 outliers final: 26 residues processed: 159 average time/residue: 0.4601 time to fit residues: 81.4622 Evaluate side-chains 157 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 296 VAL 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 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 296 VAL 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 B residue 402 SER Chi-restraints excluded: chain C residue 16 THR 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 369 LEU 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 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 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 402 SER Chi-restraints excluded: chain D residue 483 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 72 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124415 restraints weight = 45530.710| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.08 r_work: 0.3187 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0887 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= 0.119 Angle : 0.468 4.483 19412 Z= 0.251 Chirality : 0.042 0.135 2276 Planarity : 0.004 0.025 2500 Dihedral : 6.109 49.977 2120 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.18 % Allowed : 19.31 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1936 helix: 1.31 (0.18), residues: 804 sheet: -0.14 (0.26), residues: 372 loop : 0.39 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 231 TYR 0.005 0.001 TYR B 473 PHE 0.016 0.002 PHE B 125 TRP 0.016 0.002 TRP D 70 HIS 0.001 0.000 HIS C 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (14224) covalent geometry : angle 0.46785 / 0.25 (19412) hydrogen bonds : bond 0.04176 / 2.85 ( 726) hydrogen bonds : angle 4.91868 / 3.59 ( 2042) *********************** 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 159 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.497 Fit side-chains REVERT: A 312 THR cc_start: 0.7044 (t) cc_final: 0.6805 (m) REVERT: A 394 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.6365 (m-80) REVERT: B 127 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8140 (mt-10) REVERT: B 312 THR cc_start: 0.7047 (t) cc_final: 0.6809 (m) REVERT: B 394 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: C 312 THR cc_start: 0.7039 (t) cc_final: 0.6792 (m) REVERT: C 394 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: D 312 THR cc_start: 0.7038 (t) cc_final: 0.6796 (m) REVERT: D 394 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6366 (m-80) outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.5131 time to fit residues: 88.2182 Evaluate side-chains 150 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 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 C residue 402 SER 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 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 175 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.143701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.122482 restraints weight = 48478.137| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.29 r_work: 0.3146 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 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 = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14224 Z= 0.156 Angle : 0.506 4.507 19412 Z= 0.272 Chirality : 0.043 0.140 2276 Planarity : 0.004 0.024 2500 Dihedral : 6.196 49.939 2120 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.26 % Allowed : 19.31 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1936 helix: 1.31 (0.18), residues: 796 sheet: -0.15 (0.26), residues: 372 loop : 0.31 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 231 TYR 0.007 0.001 TYR D 483 PHE 0.018 0.002 PHE C 125 TRP 0.016 0.002 TRP B 70 HIS 0.002 0.001 HIS B 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (14224) covalent geometry : angle 0.50634 / 0.27 (19412) hydrogen bonds : bond 0.04746 / 3.22 ( 726) hydrogen bonds : angle 5.01904 / 3.66 ( 2042) *********************** 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 150 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.521 Fit side-chains REVERT: A 312 THR cc_start: 0.7078 (t) cc_final: 0.6836 (m) REVERT: A 394 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: B 312 THR cc_start: 0.7073 (t) cc_final: 0.6833 (m) REVERT: B 394 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: C 312 THR cc_start: 0.7067 (t) cc_final: 0.6817 (m) REVERT: C 394 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: D 312 THR cc_start: 0.7071 (t) cc_final: 0.6827 (m) REVERT: D 394 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.6409 (m-80) outliers start: 21 outliers final: 16 residues processed: 146 average time/residue: 0.5916 time to fit residues: 95.4331 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 : 0.523 ------------------------------------------------------------------------------- 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 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 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 C residue 402 SER 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 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 29 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123623 restraints weight = 49908.256| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.32 r_work: 0.3146 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 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 = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14224 Z= 0.152 Angle : 0.504 4.508 19412 Z= 0.270 Chirality : 0.042 0.139 2276 Planarity : 0.004 0.024 2500 Dihedral : 6.178 49.956 2120 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.18 % Allowed : 19.39 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1936 helix: 1.32 (0.18), residues: 796 sheet: -0.15 (0.26), residues: 372 loop : 0.33 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 231 TYR 0.006 0.001 TYR C 483 PHE 0.017 0.002 PHE B 125 TRP 0.016 0.002 TRP A 70 HIS 0.001 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (14224) covalent geometry : angle 0.50423 / 0.27 (19412) hydrogen bonds : bond 0.04675 / 3.17 ( 726) hydrogen bonds : angle 5.00922 / 3.65 ( 2042) ********************** 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 : 0.641 Fit side-chains REVERT: A 312 THR cc_start: 0.7134 (t) cc_final: 0.6901 (m) REVERT: A 394 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: B 312 THR cc_start: 0.7130 (t) cc_final: 0.6897 (m) REVERT: B 394 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: C 312 THR cc_start: 0.7130 (t) cc_final: 0.6894 (m) REVERT: C 394 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: D 312 THR cc_start: 0.7128 (t) cc_final: 0.6893 (m) REVERT: D 394 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.6473 (m-80) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 0.5801 time to fit residues: 92.4075 Evaluate side-chains 150 residues out of total 1408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 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 C residue 402 SER 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 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 5 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.143283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122886 restraints weight = 44516.582| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.12 r_work: 0.3144 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 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 = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14224 Z= 0.187 Angle : 0.541 4.507 19412 Z= 0.290 Chirality : 0.044 0.141 2276 Planarity : 0.004 0.025 2500 Dihedral : 6.320 50.242 2120 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.34 % Allowed : 19.24 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1936 helix: 1.19 (0.18), residues: 796 sheet: -0.13 (0.26), residues: 372 loop : 0.25 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.008 0.002 TYR C 483 PHE 0.019 0.002 PHE C 125 TRP 0.018 0.002 TRP A 70 HIS 0.002 0.001 HIS D 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (14224) covalent geometry : angle 0.54149 / 0.29 (19412) hydrogen bonds : bond 0.05089 / 3.45 ( 726) hydrogen bonds : angle 5.11891 / 3.73 ( 2042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4279.69 seconds wall clock time: 73 minutes 52.99 seconds (4432.99 seconds total)