Starting phenix.real_space_refine on Sun Jul 21 12:25:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/07_2024/8c54_16433.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/07_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_16433/07_2024/8c54_16433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/07_2024/8c54_16433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/07_2024/8c54_16433.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c54_16433/07_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 Residue "A ASP 41": "OD1" <-> "OD2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 14.66, per 1000 atoms: 1.03 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 - 3.50 Amino acid : False - 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: 6.46 Conformation dependent library (CDL) restraints added in 5.1 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: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 52 through 71 Processing helix chain 'A' and resid 74 through 92 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 107 through 129 removed outlier: 4.526A pdb=" N TYR A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.653A pdb=" N THR A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 172 " --> pdb=" O MET A 168 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.506A pdb=" N ILE A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 275 through 289 removed outlier: 3.674A pdb=" N ARG A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.725A pdb=" N VAL A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.761A pdb=" N LYS A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 74 through 92 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 107 through 129 removed outlier: 4.525A pdb=" N TYR B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.658A pdb=" N THR B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 172 " --> pdb=" O MET B 168 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 218 through 229 removed outlier: 3.507A pdb=" N ILE B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 251 Processing helix chain 'B' and resid 252 through 255 Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.673A pdb=" N ARG B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 357 removed outlier: 3.725A pdb=" N VAL B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.756A pdb=" N LYS B 390 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 428 through 439 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'C' and resid 11 through 15 Processing helix chain 'C' and resid 52 through 71 Processing helix chain 'C' and resid 74 through 92 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 129 removed outlier: 4.525A pdb=" N TYR C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 166 through 180 removed outlier: 3.660A pdb=" N THR C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 172 " --> pdb=" O MET C 168 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 218 through 229 removed outlier: 3.507A pdb=" N ILE C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 252 through 255 Processing helix chain 'C' and resid 275 through 289 removed outlier: 3.678A pdb=" N ARG C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 357 removed outlier: 3.724A pdb=" N VAL C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.756A pdb=" N LYS C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 Processing helix chain 'C' and resid 428 through 439 Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 52 through 71 Processing helix chain 'D' and resid 74 through 92 Processing helix chain 'D' and resid 92 through 105 Processing helix chain 'D' and resid 107 through 129 removed outlier: 4.525A pdb=" N TYR D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.659A pdb=" N THR D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS D 172 " --> pdb=" O MET D 168 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 218 through 229 removed outlier: 3.507A pdb=" N ILE D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 252 through 255 Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.677A pdb=" N ARG D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 307 through 321 removed outlier: 3.916A pdb=" N GLY D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 357 removed outlier: 3.726A pdb=" N VAL D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.772A pdb=" N LYS D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 414 Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 37 removed outlier: 5.641A pdb=" N ILE A 34 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN A 47 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 36 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.331A pdb=" N VAL C 378 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR C 377 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 400 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 379 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N SER C 402 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASN C 299 " --> pdb=" O PRO C 399 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE C 401 " --> pdb=" O ASN C 299 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE C 301 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N PHE C 403 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL C 303 " --> pdb=" O PHE C 403 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 266 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N TYR C 302 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 268 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLN C 304 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL C 270 " --> pdb=" O GLN C 304 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER C 422 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL C 444 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TYR A 483 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 446 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA A 485 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 146 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 146 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL D 444 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR B 483 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL D 446 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA B 485 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER D 422 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA D 266 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N TYR D 302 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE D 268 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLN D 304 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL D 270 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASN D 299 " --> pdb=" O PRO D 399 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE D 401 " --> pdb=" O ASN D 299 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE D 301 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE D 403 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL D 303 " --> pdb=" O PHE D 403 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR D 377 " --> pdb=" O ALA D 398 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE D 400 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 379 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER D 402 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 378 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 214 removed outlier: 6.526A pdb=" N VAL A 155 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR A 236 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ALA A 157 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR A 238 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 159 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.327A pdb=" N VAL A 378 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR A 377 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 400 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 379 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER A 402 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN A 299 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ILE A 401 " --> pdb=" O ASN A 299 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 301 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE A 403 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 303 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 266 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR A 302 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE A 268 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN A 304 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 270 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER A 422 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 146 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 146 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER B 422 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 266 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR B 302 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 268 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLN B 304 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL B 270 " --> pdb=" O GLN B 304 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN B 299 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ILE B 401 " --> pdb=" O ASN B 299 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 301 " --> pdb=" O ILE B 401 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE B 403 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 303 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 377 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE B 400 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL B 379 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N SER B 402 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 378 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 37 removed outlier: 5.657A pdb=" N ILE B 34 " --> pdb=" O ASN B 47 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 47 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 36 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 212 through 214 removed outlier: 6.514A pdb=" N VAL B 155 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR B 236 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA B 157 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR B 238 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 159 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 418 through 419 Processing sheet with id=AB2, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AB3, first strand: chain 'C' and resid 33 through 37 removed outlier: 5.642A pdb=" N ILE C 34 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASN C 47 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 36 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 212 through 214 removed outlier: 6.523A pdb=" N VAL C 155 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR C 236 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 157 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR C 238 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE C 159 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 418 through 419 Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB7, first strand: chain 'D' and resid 33 through 37 removed outlier: 5.644A pdb=" N ILE D 34 " --> pdb=" O ASN D 47 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASN D 47 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 36 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 212 through 214 removed outlier: 6.513A pdb=" N VAL D 155 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N THR D 236 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA D 157 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR D 238 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE D 159 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 418 through 419 726 hydrogen bonds defined for protein. 2042 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 6.81 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: 100.26 - 107.55: 637 107.55 - 114.84: 8410 114.84 - 122.14: 7655 122.14 - 129.43: 2630 129.43 - 136.72: 80 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 2.440 nonbonded pdb=" O CYS A 297 " pdb=" O HOH A 601 " model vdw 2.236 2.440 nonbonded pdb=" O CYS B 297 " pdb=" O HOH B 601 " model vdw 2.236 2.440 nonbonded pdb=" O CYS C 297 " pdb=" O HOH C 601 " model vdw 2.237 2.440 nonbonded pdb=" OD2 ASP A 135 " pdb=" OH TYR C 473 " model vdw 2.237 2.440 ... (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 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: 0.800 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 52.800 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.660 ------------------------------------------------------------------------------- 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 : 1.784 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 164 average time/residue: 1.0906 time to fit residues: 199.9774 Evaluate side-chains 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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: 1.9990 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: 10.0000 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14224 Z= 0.352 Angle : 0.591 4.481 19412 Z= 0.318 Chirality : 0.045 0.141 2276 Planarity : 0.005 0.031 2500 Dihedral : 9.234 81.683 2352 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.21 % Allowed : 19.78 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.19), residues: 1936 helix: 0.90 (0.19), residues: 800 sheet: -0.09 (0.26), residues: 372 loop : 0.05 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 70 HIS 0.002 0.001 HIS C 349 PHE 0.021 0.003 PHE C 424 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 176 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 1.516 Fit side-chains REVERT: A 394 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: B 394 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: C 394 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: C 483 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.7032 (t80) REVERT: D 394 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: D 483 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7031 (t80) outliers start: 46 outliers final: 28 residues processed: 168 average time/residue: 1.1714 time to fit residues: 217.8672 Evaluate side-chains 161 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 296 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP 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 B residue 408 ASP 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 408 ASP 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 408 ASP 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: 5.9990 chunk 145 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.0611 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= 0.192 Angle : 0.479 4.499 19412 Z= 0.258 Chirality : 0.042 0.135 2276 Planarity : 0.004 0.023 2500 Dihedral : 8.029 81.295 2336 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.80 % Allowed : 20.17 % Favored : 77.02 % 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: 0.87 (0.19), residues: 1936 helix: 1.28 (0.19), residues: 796 sheet: 0.07 (0.26), residues: 372 loop : 0.28 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 70 HIS 0.001 0.000 HIS A 349 PHE 0.017 0.002 PHE B 125 TYR 0.005 0.001 TYR C 483 ARG 0.002 0.000 ARG D 231 *********************** 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 174 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.582 Fit side-chains REVERT: A 394 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: B 394 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: C 394 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6457 (m-80) REVERT: D 312 THR cc_start: 0.7108 (t) cc_final: 0.6853 (m) REVERT: D 394 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6457 (m-80) outliers start: 28 outliers final: 16 residues processed: 168 average time/residue: 1.1526 time to fit residues: 214.9429 Evaluate side-chains 151 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 408 ASP 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 408 ASP 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 408 ASP 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 408 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 117 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 overall best weight: 1.5162 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.0648 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= 0.183 Angle : 0.471 4.526 19412 Z= 0.254 Chirality : 0.041 0.136 2276 Planarity : 0.004 0.024 2500 Dihedral : 7.838 82.392 2328 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.18 % Allowed : 20.79 % Favored : 77.02 % 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: 0.99 (0.19), residues: 1936 helix: 1.40 (0.19), residues: 796 sheet: 0.04 (0.25), residues: 396 loop : 0.37 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 70 HIS 0.001 0.000 HIS D 349 PHE 0.016 0.002 PHE C 125 TYR 0.005 0.001 TYR C 483 ARG 0.002 0.000 ARG C 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 156 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.488 Fit side-chains REVERT: A 312 THR cc_start: 0.7121 (t) cc_final: 0.6872 (m) REVERT: A 394 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: B 312 THR cc_start: 0.7115 (t) cc_final: 0.6865 (m) REVERT: B 394 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: C 312 THR cc_start: 0.7114 (t) cc_final: 0.6862 (m) REVERT: C 394 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: D 394 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6485 (m-80) outliers start: 20 outliers final: 16 residues processed: 152 average time/residue: 1.1635 time to fit residues: 196.2733 Evaluate side-chains 156 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 408 ASP 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 408 ASP 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 408 ASP 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 408 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 138 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14224 Z= 0.315 Angle : 0.560 4.439 19412 Z= 0.302 Chirality : 0.044 0.140 2276 Planarity : 0.005 0.026 2500 Dihedral : 8.177 79.742 2328 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.96 % Allowed : 20.33 % Favored : 76.71 % 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: 0.74 (0.19), residues: 1936 helix: 1.07 (0.19), residues: 800 sheet: 0.04 (0.25), residues: 396 loop : 0.31 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 70 HIS 0.002 0.001 HIS A 349 PHE 0.020 0.003 PHE C 125 TYR 0.008 0.002 TYR D 483 ARG 0.003 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 158 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.588 Fit side-chains REVERT: A 394 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: B 394 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: C 394 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: C 483 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.6903 (t80) REVERT: D 394 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: D 483 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.6914 (t80) outliers start: 30 outliers final: 24 residues processed: 150 average time/residue: 1.2243 time to fit residues: 203.4200 Evaluate side-chains 156 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 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 307 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP 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 307 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 408 ASP 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 307 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 394 PHE Chi-restraints excluded: chain C residue 408 ASP 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 307 VAL Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP 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: 0.2980 chunk 167 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.0683 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= 0.173 Angle : 0.464 4.487 19412 Z= 0.250 Chirality : 0.041 0.135 2276 Planarity : 0.004 0.024 2500 Dihedral : 7.818 81.822 2328 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.34 % Allowed : 20.33 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1936 helix: 1.38 (0.19), residues: 800 sheet: 0.07 (0.25), residues: 396 loop : 0.50 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 70 HIS 0.001 0.000 HIS C 349 PHE 0.017 0.002 PHE C 125 TYR 0.005 0.001 TYR B 483 ARG 0.002 0.000 ARG D 231 *********************** 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 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.517 Fit side-chains REVERT: A 312 THR cc_start: 0.7111 (t) cc_final: 0.6864 (m) REVERT: A 394 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.6494 (m-80) REVERT: B 312 THR cc_start: 0.7103 (t) cc_final: 0.6857 (m) REVERT: B 394 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: C 312 THR cc_start: 0.7103 (t) cc_final: 0.6853 (m) REVERT: C 394 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: D 312 THR cc_start: 0.7092 (t) cc_final: 0.6842 (m) REVERT: D 394 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6475 (m-80) outliers start: 22 outliers final: 17 residues processed: 160 average time/residue: 1.1399 time to fit residues: 203.0742 Evaluate side-chains 159 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 408 ASP 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 408 ASP 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 408 ASP Chi-restraints excluded: chain D residue 101 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 394 PHE Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.0630 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 : 0.486 4.521 19412 Z= 0.261 Chirality : 0.042 0.137 2276 Planarity : 0.004 0.024 2500 Dihedral : 7.857 81.649 2328 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.57 % Allowed : 20.79 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1936 helix: 1.35 (0.19), residues: 800 sheet: 0.07 (0.25), residues: 396 loop : 0.48 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 70 HIS 0.001 0.001 HIS D 349 PHE 0.018 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 163 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.696 Fit side-chains REVERT: A 394 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: B 394 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: C 394 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: D 394 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.6461 (m-80) outliers start: 25 outliers final: 19 residues processed: 159 average time/residue: 1.1603 time to fit residues: 205.0592 Evaluate side-chains 161 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 408 ASP Chi-restraints excluded: chain B residue 101 THR 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 408 ASP Chi-restraints excluded: chain C residue 101 THR 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 408 ASP Chi-restraints excluded: chain D residue 101 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 394 PHE Chi-restraints excluded: chain D residue 408 ASP 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: 0.8980 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14224 Z= 0.152 Angle : 0.447 4.529 19412 Z= 0.240 Chirality : 0.041 0.134 2276 Planarity : 0.004 0.025 2500 Dihedral : 7.689 83.620 2328 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.41 % Allowed : 20.79 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1936 helix: 1.52 (0.19), residues: 804 sheet: 0.06 (0.25), residues: 396 loop : 0.60 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 70 HIS 0.001 0.000 HIS A 405 PHE 0.015 0.001 PHE B 125 TYR 0.004 0.001 TYR A 483 ARG 0.001 0.000 ARG C 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 172 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 1.467 Fit side-chains REVERT: A 312 THR cc_start: 0.7119 (t) cc_final: 0.6874 (m) REVERT: A 394 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: B 312 THR cc_start: 0.7110 (t) cc_final: 0.6866 (m) REVERT: B 394 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: C 312 THR cc_start: 0.7112 (t) cc_final: 0.6864 (m) REVERT: C 394 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: D 312 THR cc_start: 0.7104 (t) cc_final: 0.6827 (m) REVERT: D 394 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.6463 (m-80) outliers start: 23 outliers final: 16 residues processed: 168 average time/residue: 1.1103 time to fit residues: 207.8852 Evaluate side-chains 164 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 408 ASP 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 408 ASP 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 408 ASP 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 408 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.8160 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14224 Z= 0.285 Angle : 0.538 4.502 19412 Z= 0.289 Chirality : 0.043 0.141 2276 Planarity : 0.004 0.025 2500 Dihedral : 8.057 80.591 2328 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.57 % Allowed : 20.72 % Favored : 76.71 % 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: 1.21 (0.19), residues: 800 sheet: 0.05 (0.25), residues: 396 loop : 0.45 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 70 HIS 0.002 0.001 HIS C 349 PHE 0.019 0.002 PHE C 125 TYR 0.009 0.002 TYR C 483 ARG 0.003 0.000 ARG A 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 155 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.539 Fit side-chains REVERT: A 394 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6493 (m-80) REVERT: B 394 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: C 394 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: D 394 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6478 (m-80) outliers start: 25 outliers final: 20 residues processed: 151 average time/residue: 1.1882 time to fit residues: 199.1100 Evaluate side-chains 154 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE 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 257 ARG Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 394 PHE 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 257 ARG Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 394 PHE 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 257 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 394 PHE Chi-restraints excluded: chain D residue 408 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.8126 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14224 Z= 0.166 Angle : 0.461 4.522 19412 Z= 0.248 Chirality : 0.041 0.134 2276 Planarity : 0.004 0.025 2500 Dihedral : 7.797 82.084 2328 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.34 % Allowed : 20.95 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 1936 helix: 1.44 (0.19), residues: 800 sheet: 0.05 (0.25), residues: 396 loop : 0.58 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 70 HIS 0.001 0.000 HIS B 349 PHE 0.016 0.002 PHE D 125 TYR 0.005 0.001 TYR A 483 ARG 0.001 0.000 ARG D 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 167 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.519 Fit side-chains REVERT: A 312 THR cc_start: 0.7130 (t) cc_final: 0.6884 (m) REVERT: A 394 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: B 312 THR cc_start: 0.7122 (t) cc_final: 0.6877 (m) REVERT: B 394 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: C 312 THR cc_start: 0.7122 (t) cc_final: 0.6874 (m) REVERT: C 394 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: D 312 THR cc_start: 0.7111 (t) cc_final: 0.6863 (m) REVERT: D 394 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.6472 (m-80) outliers start: 22 outliers final: 18 residues processed: 163 average time/residue: 1.1225 time to fit residues: 203.8310 Evaluate side-chains 161 residues out of total 1408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 257 ARG Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 408 ASP 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 408 ASP Chi-restraints excluded: chain C residue 101 THR 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 408 ASP 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 408 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121627 restraints weight = 46330.051| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.13 r_work: 0.3136 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14224 Z= 0.334 Angle : 0.573 4.490 19412 Z= 0.308 Chirality : 0.044 0.141 2276 Planarity : 0.005 0.026 2500 Dihedral : 8.155 79.460 2328 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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: 0.75 (0.19), residues: 1936 helix: 1.08 (0.19), residues: 800 sheet: -0.06 (0.26), residues: 364 loop : 0.36 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 70 HIS 0.002 0.001 HIS D 349 PHE 0.020 0.003 PHE B 125 TYR 0.010 0.002 TYR C 483 ARG 0.004 0.001 ARG B 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4209.78 seconds wall clock time: 74 minutes 48.73 seconds (4488.73 seconds total)