Starting phenix.real_space_refine on Fri Aug 9 22:32:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/08_2024/8bho_16063_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/08_2024/8bho_16063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/08_2024/8bho_16063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/08_2024/8bho_16063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/08_2024/8bho_16063_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bho_16063/08_2024/8bho_16063_trim.cif" } resolution = 2.93 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= 0.001 sd= 0.023 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 S 85 5.16 5 C 8925 2.51 5 N 2275 2.21 5 O 2490 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27190 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'QMJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.35, per 1000 atoms: 0.45 Number of scatterers: 27190 At special positions: 0 Unit cell: (92.4, 94.5, 123.9, 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 85 16.00 O 2490 8.00 N 2275 7.00 C 8925 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 20.06 Conformation dependent library (CDL) restraints added in 2.5 seconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 39.9% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.672A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.859A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.673A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 3.858A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.673A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.859A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.673A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 3.859A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.672A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 3.858A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 3.521A pdb=" N ALA E 321 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY A 107 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 141 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.675A pdb=" N THR A 133 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 49 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.674A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY B 107 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 141 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR B 133 " --> pdb=" O MET B 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 49 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY C 107 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU C 141 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR C 133 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 49 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 112 removed outlier: 6.735A pdb=" N GLY D 107 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU D 141 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR D 133 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 49 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.675A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 112 removed outlier: 6.734A pdb=" N GLY E 107 " --> pdb=" O GLU E 141 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU E 141 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 124 removed outlier: 3.676A pdb=" N THR E 133 " --> pdb=" O MET E 121 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR E 49 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.674A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2355 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: 9.67 Time building geometry restraints manager: 21.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 10 1.23 - 1.42: 6105 1.42 - 1.61: 7885 1.61 - 1.81: 150 Bond restraints: 27565 Sorted by residual: bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 27560 not shown) Histogram of bond angle deviations from ideal: 100.61 - 107.28: 626 107.28 - 113.96: 32078 113.96 - 120.63: 9635 120.63 - 127.31: 7006 127.31 - 133.99: 195 Bond angle restraints: 49540 Sorted by residual: angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 9.98e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.93e+00 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.37 -5.67 1.80e+00 3.09e-01 9.92e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.83e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.82e+00 ... (remaining 49535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 12611 14.62 - 29.25: 374 29.25 - 43.87: 130 43.87 - 58.49: 105 58.49 - 73.12: 15 Dihedral angle restraints: 13235 sinusoidal: 7105 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS D 315 " pdb=" CG LYS D 315 " pdb=" CD LYS D 315 " pdb=" CE LYS D 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.65 -40.65 3 1.50e+01 4.44e-03 7.25e+00 dihedral pdb=" CB LYS B 315 " pdb=" CG LYS B 315 " pdb=" CD LYS B 315 " pdb=" CE LYS B 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.64 -40.64 3 1.50e+01 4.44e-03 7.25e+00 dihedral pdb=" CB LYS C 315 " pdb=" CG LYS C 315 " pdb=" CD LYS C 315 " pdb=" CE LYS C 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.64 -40.64 3 1.50e+01 4.44e-03 7.25e+00 ... (remaining 13232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1889 0.055 - 0.111: 256 0.111 - 0.166: 15 0.166 - 0.221: 0 0.221 - 0.277: 5 Chirality restraints: 2165 Sorted by residual: chirality pdb=" C13 QMJ D 502 " pdb=" C14 QMJ D 502 " pdb=" C4 QMJ D 502 " pdb=" N2 QMJ D 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C13 QMJ C 502 " pdb=" C14 QMJ C 502 " pdb=" C4 QMJ C 502 " pdb=" N2 QMJ C 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C13 QMJ A 502 " pdb=" C14 QMJ A 502 " pdb=" C4 QMJ A 502 " pdb=" N2 QMJ A 502 " both_signs ideal model delta sigma weight residual False -2.58 -2.31 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2162 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 QMJ A 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ A 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ A 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ A 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ A 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ A 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ E 502 " 0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ E 502 " -0.032 2.00e-02 2.50e+03 pdb=" C13 QMJ E 502 " -0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ E 502 " 0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ E 502 " 0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ E 502 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 QMJ C 502 " -0.378 2.00e-02 2.50e+03 3.01e-01 1.36e+03 pdb=" C12 QMJ C 502 " 0.031 2.00e-02 2.50e+03 pdb=" C13 QMJ C 502 " 0.348 2.00e-02 2.50e+03 pdb=" C16 QMJ C 502 " -0.374 2.00e-02 2.50e+03 pdb=" N2 QMJ C 502 " -0.003 2.00e-02 2.50e+03 pdb=" O2 QMJ C 502 " 0.375 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 5486 2.31 - 2.88: 62144 2.88 - 3.45: 67787 3.45 - 4.03: 97104 4.03 - 4.60: 146582 Nonbonded interactions: 379103 Sorted by model distance: nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.735 2.450 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.735 2.450 ... (remaining 379098 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.410 Extract box with map and model: 0.950 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 81.200 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.002 0.035 14150 Z= 0.111 Angle : 0.445 8.592 19265 Z= 0.193 Chirality : 0.039 0.277 2165 Planarity : 0.014 0.301 2395 Dihedral : 7.455 73.117 5225 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 2.52 (0.22), residues: 1670 helix: 3.34 (0.21), residues: 575 sheet: 0.79 (0.27), residues: 435 loop : 0.89 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 73 HIS 0.002 0.000 HIS E 195 PHE 0.004 0.000 PHE C 149 TYR 0.004 0.001 TYR C 285 ARG 0.001 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8782 (ttm) cc_final: 0.8433 (ttm) REVERT: B 48 MET cc_start: 0.8877 (ttm) cc_final: 0.8649 (mtp) REVERT: B 289 MET cc_start: 0.8636 (ttp) cc_final: 0.8315 (ttp) REVERT: D 289 MET cc_start: 0.8606 (ttp) cc_final: 0.8395 (ttp) REVERT: E 289 MET cc_start: 0.8619 (ttp) cc_final: 0.8387 (ttp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 2.8848 time to fit residues: 503.4790 Evaluate side-chains 106 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 71 GLN B 85 GLN C 71 GLN D 71 GLN D 85 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 14150 Z= 0.431 Angle : 0.603 6.205 19265 Z= 0.325 Chirality : 0.043 0.144 2165 Planarity : 0.006 0.087 2395 Dihedral : 5.662 62.529 2090 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.81 % Allowed : 4.70 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.79 (0.21), residues: 1670 helix: 3.16 (0.21), residues: 580 sheet: 0.17 (0.25), residues: 460 loop : 0.16 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 174 HIS 0.005 0.001 HIS B 221 PHE 0.012 0.002 PHE E 229 TYR 0.012 0.001 TYR D 163 ARG 0.007 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.9096 (mmm) cc_final: 0.8826 (mmm) REVERT: A 245 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8295 (mp10) REVERT: A 301 PHE cc_start: 0.8681 (t80) cc_final: 0.8472 (t80) REVERT: D 397 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8294 (ttt) REVERT: E 397 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8023 (ttp) outliers start: 12 outliers final: 1 residues processed: 110 average time/residue: 2.6066 time to fit residues: 318.0076 Evaluate side-chains 93 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 167 ASN Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14150 Z= 0.225 Angle : 0.486 6.725 19265 Z= 0.258 Chirality : 0.040 0.142 2165 Planarity : 0.005 0.070 2395 Dihedral : 4.038 36.042 2090 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.81 % Allowed : 6.17 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.72 (0.21), residues: 1670 helix: 3.24 (0.21), residues: 580 sheet: 0.02 (0.25), residues: 435 loop : 0.05 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 73 HIS 0.002 0.001 HIS C 195 PHE 0.009 0.001 PHE C 229 TYR 0.008 0.001 TYR A 417 ARG 0.008 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8071 (mp10) REVERT: A 301 PHE cc_start: 0.8686 (t80) cc_final: 0.8473 (t80) REVERT: C 245 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: C 306 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8612 (tm-30) REVERT: D 397 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8281 (ttt) REVERT: E 397 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8085 (ttp) outliers start: 12 outliers final: 1 residues processed: 102 average time/residue: 2.7329 time to fit residues: 307.2150 Evaluate side-chains 98 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14150 Z= 0.231 Angle : 0.480 6.247 19265 Z= 0.254 Chirality : 0.040 0.141 2165 Planarity : 0.005 0.063 2395 Dihedral : 3.664 24.352 2090 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.94 % Allowed : 6.31 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.67 (0.21), residues: 1670 helix: 3.28 (0.21), residues: 580 sheet: -0.04 (0.25), residues: 430 loop : -0.03 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS B 221 PHE 0.009 0.001 PHE D 104 TYR 0.009 0.001 TYR A 417 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: A 301 PHE cc_start: 0.8678 (t80) cc_final: 0.8445 (t80) REVERT: B 239 MET cc_start: 0.9225 (mmm) cc_final: 0.8982 (mmm) REVERT: B 306 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8671 (tm-30) REVERT: C 245 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7956 (mp10) REVERT: C 306 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8637 (tm-30) REVERT: D 397 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8290 (ttt) outliers start: 14 outliers final: 1 residues processed: 107 average time/residue: 2.6281 time to fit residues: 310.7885 Evaluate side-chains 103 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 114 TRP Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain D residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 0.0050 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 14150 Z= 0.298 Angle : 0.501 5.993 19265 Z= 0.266 Chirality : 0.040 0.136 2165 Planarity : 0.005 0.088 2395 Dihedral : 4.070 25.312 2090 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.87 % Allowed : 6.04 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % 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: 1.54 (0.21), residues: 1670 helix: 3.41 (0.21), residues: 550 sheet: -0.24 (0.24), residues: 455 loop : -0.06 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.003 0.001 HIS D 221 PHE 0.012 0.001 PHE B 104 TYR 0.012 0.001 TYR A 417 ARG 0.010 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: A 301 PHE cc_start: 0.8665 (t80) cc_final: 0.8415 (t80) REVERT: B 306 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: C 245 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: D 397 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8280 (ttt) REVERT: E 27 ASP cc_start: 0.7255 (p0) cc_final: 0.7019 (p0) REVERT: E 397 MET cc_start: 0.8479 (ttm) cc_final: 0.8042 (ttp) outliers start: 13 outliers final: 3 residues processed: 108 average time/residue: 2.6326 time to fit residues: 320.0330 Evaluate side-chains 100 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLN Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 0.0970 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: