Starting phenix.real_space_refine on Thu Sep 26 23:21:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/09_2024/8c54_16433.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/09_2024/8c54_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/09_2024/8c54_16433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/09_2024/8c54_16433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/09_2024/8c54_16433.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/09_2024/8c54_16433.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 72 5.16 5 C 8884 2.51 5 N 2404 2.21 5 O 2898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14266 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "B" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "C" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "D" Number of atoms: 3440 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 482, 3422 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3464 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Time building chain proxies: 14.00, per 1000 atoms: 0.98 Number of scatterers: 14266 At special positions: 0 Unit cell: (97.4365, 103.464, 97.4365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 8 15.00 O 2898 8.00 N 2404 7.00 C 8884 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 3.5 seconds 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 18 sheets defined 46.7% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 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: 4.93 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4600 1.34 - 1.46: 2015 1.46 - 1.57: 7473 1.57 - 1.69: 12 1.69 - 1.81: 124 Bond restraints: 14224 Sorted by residual: bond pdb=" O5B NAI D 501 " pdb=" PA NAI D 501 " ideal model delta sigma weight residual 1.644 1.569 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O5B NAI B 501 " pdb=" PA NAI B 501 " ideal model delta sigma weight residual 1.644 1.570 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" O5B NAI A 501 " pdb=" PA NAI A 501 " ideal model delta sigma weight residual 1.644 1.570 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5B NAI C 501 " pdb=" PA NAI C 501 " ideal model delta sigma weight residual 1.644 1.571 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O5D NAI C 501 " pdb=" PN NAI C 501 " ideal model delta sigma weight residual 1.650 1.578 0.072 2.00e-02 2.50e+03 1.28e+01 ... (remaining 14219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 19037 1.65 - 3.30: 324 3.30 - 4.94: 39 4.94 - 6.59: 4 6.59 - 8.24: 8 Bond angle restraints: 19412 Sorted by residual: angle pdb=" O1N NAI D 501 " pdb=" PN NAI D 501 " pdb=" O2N NAI D 501 " ideal model delta sigma weight residual 123.22 114.98 8.24 3.00e+00 1.11e-01 7.54e+00 angle pdb=" O1N NAI C 501 " pdb=" PN NAI C 501 " pdb=" O2N NAI C 501 " ideal model delta sigma weight residual 123.22 114.99 8.23 3.00e+00 1.11e-01 7.53e+00 angle pdb=" O1N NAI B 501 " pdb=" PN NAI B 501 " pdb=" O2N NAI B 501 " ideal model delta sigma weight residual 123.22 115.01 8.21 3.00e+00 1.11e-01 7.49e+00 angle pdb=" O1N NAI A 501 " pdb=" PN NAI A 501 " pdb=" O2N NAI A 501 " ideal model delta sigma weight residual 123.22 115.01 8.21 3.00e+00 1.11e-01 7.48e+00 angle pdb=" PA NAI C 501 " pdb=" O3 NAI C 501 " pdb=" PN NAI C 501 " ideal model delta sigma weight residual 129.27 136.72 -7.45 3.00e+00 1.11e-01 6.17e+00 ... (remaining 19407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 7447 17.86 - 35.73: 761 35.73 - 53.59: 236 53.59 - 71.45: 84 71.45 - 89.32: 56 Dihedral angle restraints: 8584 sinusoidal: 3128 harmonic: 5456 Sorted by residual: dihedral pdb=" CA ASN A 118 " pdb=" C ASN A 118 " pdb=" N ALA A 119 " pdb=" CA ALA A 119 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASN C 118 " pdb=" C ASN C 118 " pdb=" N ALA C 119 " pdb=" CA ALA C 119 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN B 118 " pdb=" C ASN B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1343 0.029 - 0.058: 576 0.058 - 0.087: 177 0.087 - 0.116: 150 0.116 - 0.146: 30 Chirality restraints: 2276 Sorted by residual: chirality pdb=" C2B NAI D 501 " pdb=" C1B NAI D 501 " pdb=" C3B NAI D 501 " pdb=" O2B NAI D 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" C2B NAI A 501 " pdb=" C1B NAI A 501 " pdb=" C3B NAI A 501 " pdb=" O2B NAI A 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C2B NAI B 501 " pdb=" C1B NAI B 501 " pdb=" C3B NAI B 501 " pdb=" O2B NAI B 501 " both_signs ideal model delta sigma weight residual False -2.55 -2.69 0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2273 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 307 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C VAL A 307 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 307 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 308 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 307 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C VAL C 307 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL C 307 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA C 308 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 307 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C VAL D 307 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL D 307 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA D 308 " -0.008 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2644 2.77 - 3.30: 13685 3.30 - 3.83: 26919 3.83 - 4.37: 32596 4.37 - 4.90: 52840 Nonbonded interactions: 128684 Sorted by model distance: nonbonded pdb=" OH TYR A 473 " pdb=" OD2 ASP C 135 " model vdw 2.233 3.040 nonbonded pdb=" O CYS A 297 " pdb=" O HOH A 601 " model vdw 2.236 3.040 nonbonded pdb=" O CYS B 297 " pdb=" O HOH B 601 " model vdw 2.236 3.040 nonbonded pdb=" O CYS C 297 " pdb=" O HOH C 601 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP A 135 " pdb=" OH TYR C 473 " model vdw 2.237 3.040 ... (remaining 128679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) selection = (chain 'B' and (resid 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) selection = (chain 'C' and (resid 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) selection = (chain 'D' and (resid 8 through 52 or resid 54 through 129 or resid 131 through \ 181 or resid 183 through 285 or resid 287 through 489 or resid 501)) } 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: 1.060 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.250 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14224 Z= 0.291 Angle : 0.559 8.240 19412 Z= 0.279 Chirality : 0.043 0.146 2276 Planarity : 0.004 0.024 2500 Dihedral : 18.809 89.318 5112 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.43 % Allowed : 20.48 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1936 helix: 1.19 (0.19), residues: 792 sheet: -0.22 (0.25), residues: 376 loop : 0.09 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 70 HIS 0.002 0.000 HIS D 349 PHE 0.018 0.002 PHE A 125 TYR 0.008 0.001 TYR C 483 ARG 0.002 0.000 ARG B 231 *********************** 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 fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.643 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 164 average time/residue: 1.0907 time to fit residues: 199.5584 Evaluate side-chains 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 333 SER Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 163 ASN C 163 ASN D 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14224 Z= 0.394 Angle : 0.625 4.835 19412 Z= 0.336 Chirality : 0.046 0.145 2276 Planarity : 0.005 0.032 2500 Dihedral : 9.509 82.134 2352 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.36 % Allowed : 19.16 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1936 helix: 0.83 (0.18), residues: 796 sheet: -0.15 (0.26), residues: 372 loop : 0.08 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 70 HIS 0.002 0.001 HIS B 349 PHE 0.021 0.003 PHE A 125 TYR 0.009 0.002 TYR B 483 ARG 0.004 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3872 Ramachandran restraints generated. 1936 Oldfield, 0 Emsley, 1936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 1.624 Fit side-chains REVERT: A 394 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: B 394 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: C 394 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: C 483 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.6992 (t80) REVERT: D 394 PHE cc_start: 0.8010 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: D 483 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.7020 (t80) outliers start: 48 outliers final: 25 residues processed: 169 average time/residue: 1.1960 time to fit residues: 223.7764 Evaluate side-chains 159 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 483 TYR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 483 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS B 349 HIS C 349 HIS D 349 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14224 Z= 0.163 Angle : 0.468 4.501 19412 Z= 0.251 Chirality : 0.041 0.135 2276 Planarity : 0.004 0.024 2500 Dihedral : 8.101 88.160 2328 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.41 % Allowed : 20.40 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1936 helix: 1.30 (0.19), residues: 800 sheet: -0.13 (0.26), residues: 376 loop : 0.23 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 70 HIS 0.001 0.000 HIS A 349 PHE 0.016 0.002 PHE C 125 TYR 0.004 0.001 TYR B 473 ARG 0.001 0.000 ARG B 78 *********************** 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 161 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.521 Fit side-chains REVERT: A 394 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: B 394 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: C 394 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: D 394 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6436 (m-80) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 1.0976 time to fit residues: 189.9564 Evaluate side-chains 144 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 0.1980 chunk 185 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 163 ASN D 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0698 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= 0.231 Angle : 0.507 4.511 19412 Z= 0.273 Chirality : 0.042 0.140 2276 Planarity : 0.004 0.023 2500 Dihedral : 8.124 86.038 2320 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.49 % Allowed : 20.40 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1936 helix: 1.29 (0.19), residues: 796 sheet: -0.11 (0.26), residues: 372 loop : 0.21 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 70 HIS 0.001 0.000 HIS D 349 PHE 0.018 0.002 PHE B 125 TYR 0.007 0.002 TYR C 483 ARG 0.002 0.000 ARG D 231 *********************** 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 150 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 1.499 Fit side-chains REVERT: A 394 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: B 394 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: C 394 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: D 394 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.6516 (m-80) outliers start: 24 outliers final: 13 residues processed: 145 average time/residue: 1.1788 time to fit residues: 189.9472 Evaluate side-chains 139 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14224 Z= 0.428 Angle : 0.636 4.967 19412 Z= 0.344 Chirality : 0.047 0.146 2276 Planarity : 0.005 0.035 2500 Dihedral : 8.497 80.815 2320 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 19.55 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1936 helix: 0.81 (0.18), residues: 796 sheet: -0.11 (0.26), residues: 372 loop : 0.08 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 70 HIS 0.003 0.001 HIS B 349 PHE 0.023 0.003 PHE B 125 TYR 0.010 0.003 TYR C 483 ARG 0.005 0.001 ARG D 231 *********************** 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 154 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.444 Fit side-chains REVERT: A 394 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: B 394 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6517 (m-80) REVERT: C 394 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6536 (m-80) REVERT: C 483 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.7088 (t80) REVERT: D 394 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: D 483 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7085 (t80) outliers start: 30 outliers final: 23 residues processed: 145 average time/residue: 1.2801 time to fit residues: 204.8694 Evaluate side-chains 149 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 257 ARG Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 483 TYR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 257 ARG Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 483 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.4980 chunk 167 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14224 Z= 0.150 Angle : 0.455 4.492 19412 Z= 0.244 Chirality : 0.041 0.133 2276 Planarity : 0.003 0.025 2500 Dihedral : 7.955 87.625 2320 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.18 % Allowed : 19.78 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1936 helix: 1.39 (0.18), residues: 804 sheet: -0.13 (0.26), residues: 376 loop : 0.36 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 70 HIS 0.001 0.000 HIS D 405 PHE 0.017 0.001 PHE C 125 TYR 0.004 0.001 TYR A 86 ARG 0.001 0.000 ARG C 434 *********************** 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 160 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.253 Fit side-chains REVERT: A 312 THR cc_start: 0.7116 (t) cc_final: 0.6879 (m) REVERT: A 394 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 312 THR cc_start: 0.7111 (t) cc_final: 0.6874 (m) REVERT: B 394 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: C 312 THR cc_start: 0.7110 (t) cc_final: 0.6870 (m) REVERT: C 394 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: D 312 THR cc_start: 0.7099 (t) cc_final: 0.6860 (m) REVERT: D 394 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6454 (m-80) outliers start: 20 outliers final: 15 residues processed: 156 average time/residue: 1.2128 time to fit residues: 210.4076 Evaluate side-chains 147 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14224 Z= 0.204 Angle : 0.489 4.508 19412 Z= 0.263 Chirality : 0.042 0.139 2276 Planarity : 0.004 0.024 2500 Dihedral : 8.011 86.416 2320 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.65 % Allowed : 19.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1936 helix: 1.38 (0.19), residues: 796 sheet: -0.11 (0.26), residues: 372 loop : 0.33 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 70 HIS 0.001 0.000 HIS D 349 PHE 0.017 0.002 PHE C 125 TYR 0.006 0.001 TYR C 483 ARG 0.002 0.000 ARG B 231 *********************** 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 150 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.568 Fit side-chains REVERT: A 312 THR cc_start: 0.7117 (t) cc_final: 0.6878 (m) REVERT: A 394 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: B 312 THR cc_start: 0.7107 (t) cc_final: 0.6870 (m) REVERT: B 394 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: C 312 THR cc_start: 0.7110 (t) cc_final: 0.6869 (m) REVERT: C 394 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: D 312 THR cc_start: 0.7097 (t) cc_final: 0.6857 (m) REVERT: D 394 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6483 (m-80) outliers start: 26 outliers final: 16 residues processed: 143 average time/residue: 1.1544 time to fit residues: 183.7365 Evaluate side-chains 144 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14224 Z= 0.328 Angle : 0.572 4.437 19412 Z= 0.309 Chirality : 0.045 0.142 2276 Planarity : 0.005 0.026 2500 Dihedral : 8.292 81.621 2320 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.65 % Allowed : 19.39 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1936 helix: 1.07 (0.18), residues: 796 sheet: -0.13 (0.26), residues: 372 loop : 0.22 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 70 HIS 0.002 0.001 HIS D 349 PHE 0.020 0.003 PHE C 125 TYR 0.010 0.002 TYR C 483 ARG 0.003 0.001 ARG D 231 *********************** 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 150 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.522 Fit side-chains REVERT: A 394 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: B 394 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: C 394 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: D 394 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.6497 (m-80) outliers start: 26 outliers final: 21 residues processed: 141 average time/residue: 1.2837 time to fit residues: 200.1252 Evaluate side-chains 149 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 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 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 16 THR 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 369 LEU 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 177 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 163 optimal weight: 0.2980 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14224 Z= 0.187 Angle : 0.480 4.483 19412 Z= 0.258 Chirality : 0.042 0.136 2276 Planarity : 0.004 0.025 2500 Dihedral : 8.012 85.637 2320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.41 % Allowed : 19.55 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1936 helix: 1.36 (0.19), residues: 796 sheet: -0.16 (0.26), residues: 372 loop : 0.36 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 70 HIS 0.001 0.000 HIS D 349 PHE 0.017 0.002 PHE D 125 TYR 0.006 0.001 TYR A 473 ARG 0.002 0.000 ARG B 231 *********************** 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 152 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.526 Fit side-chains REVERT: A 312 THR cc_start: 0.7100 (t) cc_final: 0.6865 (m) REVERT: A 394 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6481 (m-80) REVERT: B 312 THR cc_start: 0.7095 (t) cc_final: 0.6858 (m) REVERT: B 394 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: C 312 THR cc_start: 0.7095 (t) cc_final: 0.6856 (m) REVERT: C 394 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: D 312 THR cc_start: 0.7082 (t) cc_final: 0.6843 (m) REVERT: D 394 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.6472 (m-80) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 1.2033 time to fit residues: 193.4780 Evaluate side-chains 150 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 182 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 HIS C 349 HIS D 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14224 Z= 0.177 Angle : 0.470 4.538 19412 Z= 0.253 Chirality : 0.042 0.138 2276 Planarity : 0.004 0.026 2500 Dihedral : 7.956 86.946 2320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 1936 helix: 1.42 (0.18), residues: 800 sheet: -0.15 (0.26), residues: 372 loop : 0.43 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 70 HIS 0.001 0.000 HIS A 349 PHE 0.017 0.002 PHE A 125 TYR 0.005 0.001 TYR A 473 ARG 0.001 0.000 ARG A 231 ********************** 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 151 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.727 Fit side-chains REVERT: A 312 THR cc_start: 0.7122 (t) cc_final: 0.6885 (m) REVERT: A 394 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: B 312 THR cc_start: 0.7117 (t) cc_final: 0.6880 (m) REVERT: B 394 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: C 312 THR cc_start: 0.7115 (t) cc_final: 0.6876 (m) REVERT: C 394 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: D 312 THR cc_start: 0.7103 (t) cc_final: 0.6864 (m) REVERT: D 394 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6467 (m-80) outliers start: 20 outliers final: 16 residues processed: 147 average time/residue: 1.2288 time to fit residues: 199.6017 Evaluate side-chains 152 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 162 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124904 restraints weight = 47411.821| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.19 r_work: 0.3173 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 68 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14224 Z= 0.184 Angle : 0.475 4.523 19412 Z= 0.255 Chirality : 0.042 0.138 2276 Planarity : 0.004 0.025 2500 Dihedral : 7.965 87.109 2320 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.26 % Allowed : 19.55 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 1936 helix: 1.42 (0.19), residues: 800 sheet: -0.17 (0.26), residues: 372 loop : 0.43 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 70 HIS 0.001 0.000 HIS B 349 PHE 0.017 0.002 PHE B 125 TYR 0.005 0.001 TYR D 473 ARG 0.002 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.95 seconds wall clock time: 75 minutes 26.22 seconds (4526.22 seconds total)