Starting phenix.real_space_refine on Fri Mar 15 20:36:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/03_2024/8bxf_16317.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/03_2024/8bxf_16317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/03_2024/8bxf_16317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/03_2024/8bxf_16317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/03_2024/8bxf_16317.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxf_16317/03_2024/8bxf_16317.pdb" } resolution = 3.4 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= 0.076 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8385 2.51 5 N 2041 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 107": "OD1" <-> "OD2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12692 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2517 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "B" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2527 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2524 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2527 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2527 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 7.04, per 1000 atoms: 0.55 Number of scatterers: 12692 At special positions: 0 Unit cell: (90.944, 90.16, 121.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2186 8.00 N 2041 7.00 C 8385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.04 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.04 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " distance=2.04 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 167 " " NAG B 501 " - " ASN B 167 " " NAG C 501 " - " ASN C 167 " " NAG D 501 " - " ASN D 167 " " NAG E 501 " - " ASN E 167 " Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3130 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 25 sheets defined 36.0% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.776A pdb=" N ARG A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.586A pdb=" N ASP A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 305 Processing helix chain 'A' and resid 417 through 443 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.736A pdb=" N LEU B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.586A pdb=" N ASP B 81 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 305 Processing helix chain 'B' and resid 417 through 443 Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.737A pdb=" N LEU C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 239 removed outlier: 4.782A pdb=" N MET C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 417 through 443 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.738A pdb=" N LEU D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP D 81 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) Proline residue: D 228 - end of helix Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 305 Processing helix chain 'D' and resid 417 through 443 Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.736A pdb=" N LEU E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.587A pdb=" N ASP E 81 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 239 removed outlier: 4.784A pdb=" N MET E 227 " --> pdb=" O TYR E 223 " (cutoff:3.500A) Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 240 through 242 No H-bonds generated for 'chain 'E' and resid 240 through 242' Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 305 Processing helix chain 'E' and resid 417 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 71 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN A 40 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 39 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR A 169 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 41 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN B 71 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN B 40 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 39 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR B 169 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 41 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 199 Processing sheet with id=AB2, first strand: chain 'C' and resid 88 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN C 71 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN C 40 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL C 39 " --> pdb=" O ASN C 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 41 " --> pdb=" O THR C 169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AB7, first strand: chain 'D' and resid 88 through 90 Processing sheet with id=AB8, first strand: chain 'D' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN D 71 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN D 40 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL D 39 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR D 169 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 41 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AC1, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AC2, first strand: chain 'D' and resid 197 through 199 Processing sheet with id=AC3, first strand: chain 'E' and resid 88 through 90 Processing sheet with id=AC4, first strand: chain 'E' and resid 88 through 90 removed outlier: 6.993A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 71 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN E 40 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 39 " --> pdb=" O ASN E 167 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR E 169 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL E 41 " --> pdb=" O THR E 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AC6, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AC7, first strand: chain 'E' and resid 197 through 199 695 hydrogen bonds defined for protein. 1935 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: 3.57 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3172 1.33 - 1.45: 2598 1.45 - 1.57: 7102 1.57 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 13012 Sorted by residual: bond pdb=" N LEU E 140 " pdb=" CA LEU E 140 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.24e-02 6.50e+03 4.78e+00 bond pdb=" N LEU C 140 " pdb=" CA LEU C 140 " ideal model delta sigma weight residual 1.457 1.483 -0.027 1.24e-02 6.50e+03 4.59e+00 bond pdb=" CB PHE D 425 " pdb=" CG PHE D 425 " ideal model delta sigma weight residual 1.502 1.551 -0.049 2.30e-02 1.89e+03 4.59e+00 bond pdb=" N MET D 301 " pdb=" CA MET D 301 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.54e+00 bond pdb=" CB PHE C 425 " pdb=" CG PHE C 425 " ideal model delta sigma weight residual 1.502 1.551 -0.049 2.30e-02 1.89e+03 4.52e+00 ... (remaining 13007 not shown) Histogram of bond angle deviations from ideal: 96.13 - 103.93: 185 103.93 - 111.73: 6174 111.73 - 119.53: 4813 119.53 - 127.33: 6481 127.33 - 135.12: 175 Bond angle restraints: 17828 Sorted by residual: angle pdb=" C TYR A 199 " pdb=" N ASN A 200 " pdb=" CA ASN A 200 " ideal model delta sigma weight residual 122.08 127.82 -5.74 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C TYR E 199 " pdb=" N ASN E 200 " pdb=" CA ASN E 200 " ideal model delta sigma weight residual 122.08 127.81 -5.73 1.47e+00 4.63e-01 1.52e+01 angle pdb=" C TYR C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta sigma weight residual 122.08 127.74 -5.66 1.47e+00 4.63e-01 1.48e+01 angle pdb=" C TYR D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta sigma weight residual 122.08 127.72 -5.64 1.47e+00 4.63e-01 1.47e+01 angle pdb=" C TYR B 199 " pdb=" N ASN B 200 " pdb=" CA ASN B 200 " ideal model delta sigma weight residual 122.08 127.71 -5.63 1.47e+00 4.63e-01 1.47e+01 ... (remaining 17823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 6828 15.42 - 30.83: 614 30.83 - 46.25: 179 46.25 - 61.66: 20 61.66 - 77.08: 15 Dihedral angle restraints: 7656 sinusoidal: 2816 harmonic: 4840 Sorted by residual: dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.24 45.76 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CB CYS B 138 " pdb=" SG CYS B 138 " pdb=" SG CYS B 152 " pdb=" CB CYS B 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.24 45.76 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 47.26 45.74 1 1.00e+01 1.00e-02 2.90e+01 ... (remaining 7653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1462 0.047 - 0.093: 498 0.093 - 0.140: 171 0.140 - 0.186: 34 0.186 - 0.233: 20 Chirality restraints: 2185 Sorted by residual: chirality pdb=" CA MET E 227 " pdb=" N MET E 227 " pdb=" C MET E 227 " pdb=" CB MET E 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA MET A 227 " pdb=" N MET A 227 " pdb=" C MET A 227 " pdb=" CB MET A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA MET D 227 " pdb=" N MET D 227 " pdb=" C MET D 227 " pdb=" CB MET D 227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2182 not shown) Planarity restraints: 2151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 425 " 0.016 2.00e-02 2.50e+03 2.39e-02 9.96e+00 pdb=" CG PHE E 425 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 425 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE E 425 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE E 425 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 425 " 0.016 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE B 425 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 425 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 425 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 425 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 425 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 425 " -0.016 2.00e-02 2.50e+03 2.37e-02 9.84e+00 pdb=" CG PHE D 425 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D 425 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 425 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE D 425 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 425 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 425 " 0.001 2.00e-02 2.50e+03 ... (remaining 2148 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 4363 2.87 - 3.38: 11502 3.38 - 3.89: 21098 3.89 - 4.39: 22881 4.39 - 4.90: 40701 Nonbonded interactions: 100545 Sorted by model distance: nonbonded pdb=" O VAL A 257 " pdb=" OG1 THR A 261 " model vdw 2.365 2.440 nonbonded pdb=" O VAL E 257 " pdb=" OG1 THR E 261 " model vdw 2.366 2.440 nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 261 " model vdw 2.366 2.440 nonbonded pdb=" O VAL C 257 " pdb=" OG1 THR C 261 " model vdw 2.366 2.440 nonbonded pdb=" O VAL D 257 " pdb=" OG1 THR D 261 " model vdw 2.367 2.440 ... (remaining 100540 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' selection = (chain 'B' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 443 or resid 501)) selection = (chain 'C' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 443 or resid 501)) selection = (chain 'D' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 443 or resid 501)) selection = (chain 'E' and (resid 12 through 171 or (resid 172 through 173 and (name N or na \ me CA or name C or name O or name CB )) or resid 174 through 199 or (resid 200 t \ hrough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 \ through 443 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=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: 2.450 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: 10.000 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 33.910 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.005 0.049 13012 Z= 0.298 Angle : 0.957 10.124 17828 Z= 0.503 Chirality : 0.056 0.233 2185 Planarity : 0.007 0.043 2146 Dihedral : 13.512 77.077 4511 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.38 % Allowed : 1.51 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.13 (0.19), residues: 1610 helix: -0.93 (0.19), residues: 530 sheet: -1.31 (0.25), residues: 450 loop : -1.72 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 70 HIS 0.021 0.003 HIS C 58 PHE 0.054 0.004 PHE E 425 TYR 0.014 0.001 TYR B 178 ARG 0.002 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 306 time to evaluate : 1.432 Fit side-chains REVERT: A 219 ILE cc_start: 0.8458 (tt) cc_final: 0.8191 (tt) REVERT: A 222 GLN cc_start: 0.8353 (mt0) cc_final: 0.8075 (mt0) REVERT: A 301 MET cc_start: 0.7955 (tmm) cc_final: 0.7699 (tmm) REVERT: B 219 ILE cc_start: 0.8474 (tt) cc_final: 0.8209 (tt) REVERT: B 222 GLN cc_start: 0.8269 (mt0) cc_final: 0.7959 (mt0) REVERT: B 301 MET cc_start: 0.7904 (tmm) cc_final: 0.7624 (tmm) REVERT: C 219 ILE cc_start: 0.8332 (tt) cc_final: 0.7954 (tp) REVERT: C 301 MET cc_start: 0.7964 (tmm) cc_final: 0.7710 (tmm) REVERT: D 16 ARG cc_start: 0.8746 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: D 66 ILE cc_start: 0.8897 (pt) cc_final: 0.8654 (pt) REVERT: D 219 ILE cc_start: 0.8457 (tt) cc_final: 0.8161 (tt) REVERT: D 222 GLN cc_start: 0.8311 (mt0) cc_final: 0.7869 (mp10) REVERT: D 301 MET cc_start: 0.7960 (tmm) cc_final: 0.7637 (tmm) REVERT: E 219 ILE cc_start: 0.8358 (tt) cc_final: 0.8092 (tt) REVERT: E 222 GLN cc_start: 0.8354 (mt0) cc_final: 0.8079 (mt0) REVERT: E 301 MET cc_start: 0.7926 (tmm) cc_final: 0.7583 (tmm) outliers start: 5 outliers final: 0 residues processed: 311 average time/residue: 0.2625 time to fit residues: 113.6822 Evaluate side-chains 232 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 0.0060 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 0.1980 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 13012 Z= 0.180 Angle : 0.555 7.871 17828 Z= 0.282 Chirality : 0.043 0.136 2185 Planarity : 0.004 0.029 2146 Dihedral : 4.435 18.394 1870 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.29 % Allowed : 11.66 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.07 (0.21), residues: 1610 helix: 0.69 (0.21), residues: 535 sheet: -1.35 (0.25), residues: 450 loop : -1.32 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 70 HIS 0.003 0.001 HIS A 58 PHE 0.012 0.001 PHE A 241 TYR 0.007 0.001 TYR B 121 ARG 0.005 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 246 time to evaluate : 1.446 Fit side-chains REVERT: A 127 MET cc_start: 0.7095 (mtt) cc_final: 0.6861 (mtp) REVERT: A 222 GLN cc_start: 0.8442 (mt0) cc_final: 0.8181 (mt0) REVERT: A 269 ASP cc_start: 0.8722 (t0) cc_final: 0.8427 (t0) REVERT: A 301 MET cc_start: 0.7937 (tmm) cc_final: 0.7622 (tmm) REVERT: B 127 MET cc_start: 0.7220 (mtt) cc_final: 0.6943 (mtp) REVERT: B 222 GLN cc_start: 0.8350 (mt0) cc_final: 0.8086 (mt0) REVERT: B 227 MET cc_start: 0.8460 (ppp) cc_final: 0.8122 (ppp) REVERT: B 301 MET cc_start: 0.7971 (tmm) cc_final: 0.7720 (tmm) REVERT: C 219 ILE cc_start: 0.8089 (tt) cc_final: 0.7823 (tt) REVERT: C 301 MET cc_start: 0.8006 (tmm) cc_final: 0.7702 (tmm) REVERT: D 127 MET cc_start: 0.7134 (mtt) cc_final: 0.6884 (mtp) REVERT: D 219 ILE cc_start: 0.8044 (tt) cc_final: 0.7798 (tt) REVERT: D 222 GLN cc_start: 0.8330 (mt0) cc_final: 0.8015 (mt0) REVERT: D 265 MET cc_start: 0.7094 (ttt) cc_final: 0.6738 (ttm) REVERT: D 266 MET cc_start: 0.7872 (mtt) cc_final: 0.7654 (mtt) REVERT: D 301 MET cc_start: 0.8021 (tmm) cc_final: 0.7717 (tmm) REVERT: E 117 LEU cc_start: 0.7901 (mm) cc_final: 0.7571 (mm) REVERT: E 222 GLN cc_start: 0.8323 (mt0) cc_final: 0.7937 (mt0) REVERT: E 265 MET cc_start: 0.7034 (ttt) cc_final: 0.6680 (ttm) REVERT: E 301 MET cc_start: 0.7920 (tmm) cc_final: 0.7608 (tmm) outliers start: 17 outliers final: 7 residues processed: 254 average time/residue: 0.2137 time to fit residues: 81.3375 Evaluate side-chains 231 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 224 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 140 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13012 Z= 0.317 Angle : 0.620 8.757 17828 Z= 0.310 Chirality : 0.044 0.144 2185 Planarity : 0.004 0.027 2146 Dihedral : 4.224 17.045 1870 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.80 % Allowed : 16.12 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1610 helix: 1.39 (0.22), residues: 535 sheet: -1.53 (0.24), residues: 465 loop : -1.12 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 65 HIS 0.006 0.001 HIS A 58 PHE 0.011 0.001 PHE A 298 TYR 0.013 0.001 TYR C 252 ARG 0.002 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 1.310 Fit side-chains REVERT: A 127 MET cc_start: 0.7084 (mtt) cc_final: 0.6850 (mtp) REVERT: A 223 TYR cc_start: 0.8339 (t80) cc_final: 0.7955 (t80) REVERT: A 248 GLU cc_start: 0.7329 (pm20) cc_final: 0.7056 (pm20) REVERT: A 265 MET cc_start: 0.6954 (ttt) cc_final: 0.6681 (ttp) REVERT: A 269 ASP cc_start: 0.8715 (t0) cc_final: 0.8339 (t0) REVERT: A 301 MET cc_start: 0.7904 (tmm) cc_final: 0.7452 (tmm) REVERT: B 222 GLN cc_start: 0.8381 (mt0) cc_final: 0.8135 (mt0) REVERT: B 265 MET cc_start: 0.8396 (ttm) cc_final: 0.7729 (mtp) REVERT: C 183 LYS cc_start: 0.8293 (ptpt) cc_final: 0.7810 (mtmt) REVERT: C 301 MET cc_start: 0.7996 (tmm) cc_final: 0.7696 (tmm) REVERT: D 87 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8396 (ttmm) REVERT: D 127 MET cc_start: 0.7179 (mtt) cc_final: 0.6878 (mtp) REVERT: D 301 MET cc_start: 0.8051 (tmm) cc_final: 0.7821 (tmm) REVERT: E 301 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7824 (tmm) outliers start: 37 outliers final: 19 residues processed: 245 average time/residue: 0.2378 time to fit residues: 87.7833 Evaluate side-chains 238 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 217 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 301 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.0470 chunk 41 optimal weight: 3.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13012 Z= 0.273 Angle : 0.584 7.822 17828 Z= 0.293 Chirality : 0.044 0.139 2185 Planarity : 0.003 0.026 2146 Dihedral : 3.981 15.466 1870 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.57 % Allowed : 19.53 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.39 (0.22), residues: 1610 helix: 1.66 (0.23), residues: 535 sheet: -1.51 (0.25), residues: 455 loop : -0.84 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 65 HIS 0.004 0.001 HIS D 58 PHE 0.010 0.001 PHE C 298 TYR 0.009 0.001 TYR C 67 ARG 0.002 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.478 Fit side-chains REVERT: A 127 MET cc_start: 0.7067 (mtt) cc_final: 0.6796 (mtp) REVERT: A 269 ASP cc_start: 0.8725 (t0) cc_final: 0.8339 (t0) REVERT: A 301 MET cc_start: 0.7962 (tmm) cc_final: 0.7686 (tmm) REVERT: B 222 GLN cc_start: 0.8383 (mt0) cc_final: 0.8160 (mt0) REVERT: B 227 MET cc_start: 0.8619 (ppp) cc_final: 0.8415 (tmm) REVERT: B 265 MET cc_start: 0.8506 (ttm) cc_final: 0.7790 (mtp) REVERT: B 301 MET cc_start: 0.7915 (tmm) cc_final: 0.7434 (tmm) REVERT: B 305 MET cc_start: 0.7396 (ptp) cc_final: 0.6878 (ptp) REVERT: C 183 LYS cc_start: 0.8362 (ptpt) cc_final: 0.7908 (mtmt) REVERT: C 245 LEU cc_start: 0.8443 (mm) cc_final: 0.7811 (pt) REVERT: C 301 MET cc_start: 0.7859 (tmm) cc_final: 0.7320 (tmm) REVERT: C 305 MET cc_start: 0.7609 (ptp) cc_final: 0.7092 (ptp) REVERT: D 87 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8404 (ttmm) REVERT: D 127 MET cc_start: 0.7117 (mtt) cc_final: 0.6840 (mtp) REVERT: D 265 MET cc_start: 0.7152 (ttt) cc_final: 0.6941 (ttm) REVERT: E 183 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8107 (mtmm) outliers start: 34 outliers final: 16 residues processed: 257 average time/residue: 0.2136 time to fit residues: 82.7964 Evaluate side-chains 244 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 248 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 0.0770 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13012 Z= 0.165 Angle : 0.555 8.282 17828 Z= 0.273 Chirality : 0.042 0.134 2185 Planarity : 0.003 0.031 2146 Dihedral : 3.834 17.807 1870 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.65 % Allowed : 20.06 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.12 (0.22), residues: 1610 helix: 1.91 (0.22), residues: 535 sheet: -1.36 (0.25), residues: 450 loop : -0.73 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 70 HIS 0.005 0.001 HIS A 68 PHE 0.007 0.001 PHE A 298 TYR 0.009 0.001 TYR D 223 ARG 0.002 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.790 Fit side-chains REVERT: A 117 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7715 (mm) REVERT: A 127 MET cc_start: 0.7011 (mtt) cc_final: 0.6795 (mtp) REVERT: A 223 TYR cc_start: 0.8337 (t80) cc_final: 0.7946 (t80) REVERT: A 269 ASP cc_start: 0.8723 (t0) cc_final: 0.8348 (t0) REVERT: A 301 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7762 (tmm) REVERT: A 431 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7577 (tt) REVERT: B 66 ILE cc_start: 0.8734 (pt) cc_final: 0.8481 (pt) REVERT: B 127 MET cc_start: 0.7150 (mtt) cc_final: 0.6835 (mtp) REVERT: B 183 LYS cc_start: 0.8370 (ptpt) cc_final: 0.7849 (mtmt) REVERT: B 184 GLU cc_start: 0.8350 (tp30) cc_final: 0.8142 (tp30) REVERT: B 222 GLN cc_start: 0.8333 (mt0) cc_final: 0.8130 (mt0) REVERT: B 245 LEU cc_start: 0.8452 (mm) cc_final: 0.7691 (pt) REVERT: B 265 MET cc_start: 0.8339 (ttm) cc_final: 0.8094 (mtp) REVERT: B 431 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7503 (tt) REVERT: C 183 LYS cc_start: 0.8362 (ptpt) cc_final: 0.7936 (mtmt) REVERT: C 245 LEU cc_start: 0.8419 (mm) cc_final: 0.7782 (pt) REVERT: C 301 MET cc_start: 0.7871 (tmm) cc_final: 0.7591 (tmm) REVERT: D 87 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8390 (ttmm) REVERT: D 117 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7743 (mm) REVERT: D 127 MET cc_start: 0.6974 (mtt) cc_final: 0.6709 (mtp) REVERT: D 265 MET cc_start: 0.7242 (ttt) cc_final: 0.6756 (mtp) REVERT: E 19 LYS cc_start: 0.9041 (ttpt) cc_final: 0.8821 (ttpp) REVERT: E 183 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8144 (mtmm) outliers start: 35 outliers final: 14 residues processed: 256 average time/residue: 0.2192 time to fit residues: 84.1489 Evaluate side-chains 247 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 226 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 0.0470 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN C 222 GLN D 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13012 Z= 0.284 Angle : 0.614 8.618 17828 Z= 0.301 Chirality : 0.044 0.162 2185 Planarity : 0.003 0.024 2146 Dihedral : 3.912 15.347 1870 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.18 % Allowed : 21.42 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.14 (0.22), residues: 1610 helix: 1.91 (0.23), residues: 535 sheet: -1.37 (0.25), residues: 455 loop : -0.74 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 65 HIS 0.006 0.001 HIS A 68 PHE 0.010 0.001 PHE A 298 TYR 0.012 0.001 TYR E 67 ARG 0.002 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 245 time to evaluate : 1.448 Fit side-chains REVERT: A 117 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7763 (mm) REVERT: A 127 MET cc_start: 0.7080 (mtt) cc_final: 0.6836 (mtp) REVERT: A 245 LEU cc_start: 0.8466 (mm) cc_final: 0.7652 (pt) REVERT: A 269 ASP cc_start: 0.8731 (t0) cc_final: 0.8348 (t0) REVERT: A 431 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7675 (tt) REVERT: B 127 MET cc_start: 0.7188 (mtt) cc_final: 0.6862 (mtp) REVERT: B 183 LYS cc_start: 0.8401 (ptpt) cc_final: 0.7863 (mtmt) REVERT: B 222 GLN cc_start: 0.8368 (mt0) cc_final: 0.8164 (mt0) REVERT: B 245 LEU cc_start: 0.8613 (mm) cc_final: 0.7793 (pt) REVERT: B 265 MET cc_start: 0.8432 (ttm) cc_final: 0.7833 (mtp) REVERT: B 305 MET cc_start: 0.7383 (ptp) cc_final: 0.7005 (ptp) REVERT: B 431 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7511 (tt) REVERT: C 66 ILE cc_start: 0.8877 (pt) cc_final: 0.8652 (pt) REVERT: C 183 LYS cc_start: 0.8351 (ptpt) cc_final: 0.8003 (mtmt) REVERT: C 231 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8454 (tt) REVERT: C 301 MET cc_start: 0.7993 (tmm) cc_final: 0.7641 (tmm) REVERT: D 87 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8420 (ttmm) REVERT: D 117 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7797 (mm) REVERT: D 127 MET cc_start: 0.7105 (mtt) cc_final: 0.6866 (mtp) REVERT: D 150 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6529 (mm-40) REVERT: D 231 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8476 (tp) REVERT: E 183 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8207 (mtmm) outliers start: 42 outliers final: 19 residues processed: 269 average time/residue: 0.2203 time to fit residues: 89.5217 Evaluate side-chains 264 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 71 optimal weight: 0.0020 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13012 Z= 0.167 Angle : 0.565 8.856 17828 Z= 0.276 Chirality : 0.042 0.139 2185 Planarity : 0.003 0.028 2146 Dihedral : 3.720 16.653 1870 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.80 % Allowed : 22.26 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.02 (0.22), residues: 1610 helix: 2.06 (0.22), residues: 535 sheet: -1.30 (0.24), residues: 455 loop : -0.66 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.006 0.001 HIS A 68 PHE 0.007 0.001 PHE E 289 TYR 0.008 0.001 TYR D 67 ARG 0.001 0.000 ARG E 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 248 time to evaluate : 1.517 Fit side-chains REVERT: A 117 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7719 (mm) REVERT: A 127 MET cc_start: 0.6985 (mtt) cc_final: 0.6781 (mtp) REVERT: A 245 LEU cc_start: 0.8404 (mm) cc_final: 0.7582 (pt) REVERT: A 269 ASP cc_start: 0.8728 (t0) cc_final: 0.8360 (t0) REVERT: A 431 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7642 (tt) REVERT: B 127 MET cc_start: 0.7050 (mtt) cc_final: 0.6767 (mtp) REVERT: B 245 LEU cc_start: 0.8590 (mm) cc_final: 0.7833 (pt) REVERT: B 305 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6946 (ptp) REVERT: B 431 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7521 (tt) REVERT: C 66 ILE cc_start: 0.8943 (pt) cc_final: 0.8677 (pt) REVERT: C 183 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8098 (mtmm) REVERT: C 245 LEU cc_start: 0.8558 (mm) cc_final: 0.7668 (pt) REVERT: C 301 MET cc_start: 0.7951 (tmm) cc_final: 0.7647 (tmm) REVERT: D 19 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8634 (mtpp) REVERT: D 87 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8388 (ttmm) REVERT: D 117 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7712 (mm) REVERT: D 127 MET cc_start: 0.6948 (mtt) cc_final: 0.6700 (mtp) REVERT: D 245 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7762 (pt) REVERT: D 265 MET cc_start: 0.7448 (ttt) cc_final: 0.6919 (mtp) REVERT: E 66 ILE cc_start: 0.8726 (pt) cc_final: 0.8478 (pt) REVERT: E 183 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8297 (mtmm) REVERT: E 245 LEU cc_start: 0.8421 (mm) cc_final: 0.7557 (pt) outliers start: 37 outliers final: 19 residues processed: 270 average time/residue: 0.2047 time to fit residues: 84.3480 Evaluate side-chains 261 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 234 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13012 Z= 0.370 Angle : 0.657 9.467 17828 Z= 0.321 Chirality : 0.046 0.147 2185 Planarity : 0.003 0.025 2146 Dihedral : 4.015 15.571 1870 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.79 % Allowed : 21.65 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.18 (0.22), residues: 1610 helix: 1.89 (0.23), residues: 535 sheet: -1.32 (0.25), residues: 455 loop : -0.86 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 65 HIS 0.013 0.001 HIS D 58 PHE 0.012 0.001 PHE A 145 TYR 0.016 0.001 TYR D 223 ARG 0.002 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 241 time to evaluate : 1.512 Fit side-chains REVERT: A 117 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7797 (mm) REVERT: A 127 MET cc_start: 0.7124 (mtt) cc_final: 0.6849 (mtp) REVERT: A 183 LYS cc_start: 0.8513 (ptpt) cc_final: 0.8172 (ptmt) REVERT: A 265 MET cc_start: 0.7534 (ttp) cc_final: 0.7108 (mtp) REVERT: A 269 ASP cc_start: 0.8722 (t0) cc_final: 0.8331 (t0) REVERT: A 431 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7729 (tt) REVERT: B 127 MET cc_start: 0.7164 (mtt) cc_final: 0.6855 (mtp) REVERT: B 305 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7002 (ptp) REVERT: B 431 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7580 (tt) REVERT: C 66 ILE cc_start: 0.8888 (pt) cc_final: 0.8662 (pt) REVERT: C 183 LYS cc_start: 0.8352 (ptpt) cc_final: 0.8105 (mtmm) REVERT: C 231 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 245 LEU cc_start: 0.8676 (mm) cc_final: 0.7826 (pt) REVERT: C 289 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8383 (t80) REVERT: C 301 MET cc_start: 0.7988 (tmm) cc_final: 0.7713 (tmm) REVERT: D 19 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8657 (mtpp) REVERT: D 117 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7841 (mm) REVERT: D 127 MET cc_start: 0.7158 (mtt) cc_final: 0.6837 (mtp) REVERT: D 231 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8475 (tp) REVERT: E 66 ILE cc_start: 0.8759 (pt) cc_final: 0.8547 (pt) REVERT: E 183 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8329 (mtmm) REVERT: E 245 LEU cc_start: 0.8576 (mm) cc_final: 0.7725 (pt) REVERT: E 266 MET cc_start: 0.7915 (mtt) cc_final: 0.7611 (mtt) outliers start: 50 outliers final: 30 residues processed: 272 average time/residue: 0.2120 time to fit residues: 86.7257 Evaluate side-chains 271 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 289 PHE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 0.3980 chunk 143 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13012 Z= 0.179 Angle : 0.595 9.264 17828 Z= 0.287 Chirality : 0.043 0.140 2185 Planarity : 0.003 0.026 2146 Dihedral : 3.794 16.131 1870 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.42 % Allowed : 23.62 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.02 (0.22), residues: 1610 helix: 2.08 (0.22), residues: 535 sheet: -1.22 (0.25), residues: 455 loop : -0.75 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.006 0.001 HIS A 68 PHE 0.014 0.001 PHE E 425 TYR 0.018 0.001 TYR D 223 ARG 0.005 0.000 ARG C 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 1.479 Fit side-chains REVERT: A 117 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7752 (mm) REVERT: A 127 MET cc_start: 0.7009 (mtt) cc_final: 0.6778 (mtp) REVERT: A 265 MET cc_start: 0.7379 (ttp) cc_final: 0.6831 (mtp) REVERT: A 431 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7680 (tt) REVERT: B 19 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8665 (mtpp) REVERT: B 127 MET cc_start: 0.7054 (mtt) cc_final: 0.6729 (mtp) REVERT: B 227 MET cc_start: 0.8446 (ppp) cc_final: 0.8214 (tmm) REVERT: B 265 MET cc_start: 0.7186 (ttt) cc_final: 0.6856 (ttm) REVERT: B 305 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6940 (ptp) REVERT: B 431 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7528 (tt) REVERT: C 66 ILE cc_start: 0.8929 (pt) cc_final: 0.8671 (pt) REVERT: C 183 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8201 (mtmm) REVERT: C 265 MET cc_start: 0.7089 (ttt) cc_final: 0.6497 (ttm) REVERT: C 301 MET cc_start: 0.7954 (tmm) cc_final: 0.7675 (tmm) REVERT: D 19 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8617 (mtpp) REVERT: D 117 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7791 (mm) REVERT: D 127 MET cc_start: 0.6952 (mtt) cc_final: 0.6691 (mtp) REVERT: D 265 MET cc_start: 0.7449 (ttt) cc_final: 0.6911 (mtp) REVERT: E 19 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8713 (mtpp) REVERT: E 66 ILE cc_start: 0.8752 (pt) cc_final: 0.8524 (pt) REVERT: E 245 LEU cc_start: 0.8530 (mm) cc_final: 0.7721 (pt) REVERT: E 266 MET cc_start: 0.7756 (mtt) cc_final: 0.7524 (mtt) outliers start: 32 outliers final: 22 residues processed: 254 average time/residue: 0.2116 time to fit residues: 80.9838 Evaluate side-chains 256 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0980 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13012 Z= 0.147 Angle : 0.585 9.923 17828 Z= 0.279 Chirality : 0.043 0.136 2185 Planarity : 0.003 0.029 2146 Dihedral : 3.660 16.174 1870 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.82 % Allowed : 24.07 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.09 (0.22), residues: 1610 helix: 2.12 (0.22), residues: 535 sheet: -1.15 (0.25), residues: 445 loop : -0.73 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 70 HIS 0.006 0.001 HIS A 68 PHE 0.009 0.001 PHE C 289 TYR 0.019 0.001 TYR D 223 ARG 0.003 0.000 ARG B 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 239 time to evaluate : 1.486 Fit side-chains REVERT: A 19 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8517 (mtpp) REVERT: A 117 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7698 (mm) REVERT: A 265 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6786 (mtp) REVERT: A 269 ASP cc_start: 0.8735 (t0) cc_final: 0.8516 (t0) REVERT: A 431 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 19 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8651 (mtpp) REVERT: B 127 MET cc_start: 0.6924 (mtt) cc_final: 0.6620 (mtp) REVERT: B 305 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7024 (ptp) REVERT: B 431 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7520 (tt) REVERT: C 66 ILE cc_start: 0.8909 (pt) cc_final: 0.8647 (pt) REVERT: C 301 MET cc_start: 0.7895 (tmm) cc_final: 0.7617 (tmm) REVERT: D 19 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8585 (mtpp) REVERT: D 117 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7738 (mm) REVERT: D 219 ILE cc_start: 0.8251 (tt) cc_final: 0.8020 (tt) REVERT: D 265 MET cc_start: 0.7440 (ttt) cc_final: 0.6907 (mtp) REVERT: E 19 LYS cc_start: 0.9070 (ttpp) cc_final: 0.8685 (mtpp) REVERT: E 66 ILE cc_start: 0.8675 (pt) cc_final: 0.8440 (pt) outliers start: 24 outliers final: 13 residues processed: 254 average time/residue: 0.2034 time to fit residues: 78.3174 Evaluate side-chains 250 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 254 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS D 222 GLN E 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.139563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.113508 restraints weight = 19768.841| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.01 r_work: 0.3363 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13012 Z= 0.145 Angle : 0.580 10.440 17828 Z= 0.276 Chirality : 0.042 0.138 2185 Planarity : 0.003 0.032 2146 Dihedral : 3.560 16.648 1870 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.74 % Allowed : 24.45 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.22 (0.22), residues: 1610 helix: 2.19 (0.22), residues: 535 sheet: -1.03 (0.25), residues: 445 loop : -0.67 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 70 HIS 0.005 0.001 HIS A 68 PHE 0.009 0.001 PHE A 289 TYR 0.023 0.001 TYR D 223 ARG 0.002 0.000 ARG E 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.20 seconds wall clock time: 50 minutes 22.66 seconds (3022.66 seconds total)