Starting phenix.real_space_refine on Thu Feb 15 14:37:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxe_16316/02_2024/8bxe_16316.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxe_16316/02_2024/8bxe_16316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxe_16316/02_2024/8bxe_16316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxe_16316/02_2024/8bxe_16316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxe_16316/02_2024/8bxe_16316.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bxe_16316/02_2024/8bxe_16316.pdb" } resolution = 3.9 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= 0.002 sd= 0.047 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 76 5.16 5 C 8319 2.51 5 N 2032 2.21 5 O 2123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 13": "OD1" <-> "OD2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 13": "OD1" <-> "OD2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 13": "OD1" <-> "OD2" Residue "D TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E ASP 269": "OD1" <-> "OD2" Residue "E PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12550 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2499 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2502 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "D" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2489 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2493 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 102 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 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.89, per 1000 atoms: 0.55 Number of scatterers: 12550 At special positions: 0 Unit cell: (89.6328, 91.152, 124.574, 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 76 16.00 O 2123 8.00 N 2032 7.00 C 8319 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=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 152 " 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 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: 5.39 Conformation dependent library (CDL) restraints added in 2.5 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: 42 helices and 20 sheets defined 38.4% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 219 through 238 removed outlier: 4.490A 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 239 through 242 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.774A pdb=" N LYS A 247 " --> pdb=" O PRO A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 Processing helix chain 'A' and resid 279 through 307 Processing helix chain 'A' and resid 416 through 441 removed outlier: 3.669A pdb=" N ILE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 219 through 239 removed outlier: 4.589A 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 243 through 247 removed outlier: 3.679A pdb=" N LYS B 247 " --> pdb=" O PRO B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Processing helix chain 'B' and resid 279 through 307 removed outlier: 3.716A pdb=" N MET B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 441 removed outlier: 3.576A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 219 through 238 removed outlier: 4.311A 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 239 through 242 Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.797A pdb=" N LYS C 247 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 271 Processing helix chain 'C' and resid 279 through 307 Processing helix chain 'C' and resid 416 through 441 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.993A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 219 through 238 removed outlier: 4.626A 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 239 through 242 removed outlier: 3.544A pdb=" N ILE D 242 " --> pdb=" O MET D 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.801A pdb=" N LYS D 247 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Processing helix chain 'D' and resid 279 through 307 removed outlier: 3.566A pdb=" N MET D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 441 removed outlier: 3.539A pdb=" N ILE D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.755A pdb=" N ASP E 81 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 Processing helix chain 'E' and resid 219 through 238 removed outlier: 4.374A 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 239 through 242 Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.794A pdb=" N LYS E 247 " --> pdb=" O PRO E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 Processing helix chain 'E' and resid 279 through 307 removed outlier: 3.588A pdb=" N MET E 307 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 441 removed outlier: 3.685A pdb=" N ILE E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.549A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.549A pdb=" N TRP A 70 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A 59 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 52 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR A 61 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN A 63 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 69 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.617A pdb=" N ILE A 88 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.747A pdb=" N GLY A 207 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 194 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 209 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 211 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.620A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 126 removed outlier: 3.620A pdb=" N VAL B 126 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP B 70 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 59 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 52 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N THR B 61 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN B 63 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 69 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.751A pdb=" N ILE B 88 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.759A pdb=" N GLY B 207 " --> pdb=" O ARG B 194 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 209 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 211 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.600A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.600A pdb=" N VAL C 126 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 70 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL C 59 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP C 52 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR C 61 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL C 50 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C 63 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU C 69 " --> pdb=" O ALA C 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.592A pdb=" N ILE C 88 " --> pdb=" O VAL C 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.780A pdb=" N GLY C 207 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG C 194 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 209 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C 211 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.596A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 126 removed outlier: 3.596A pdb=" N VAL D 126 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP D 70 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 59 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP D 52 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N THR D 61 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN D 63 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 69 " --> pdb=" O ALA D 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 88 through 90 removed outlier: 3.517A pdb=" N ILE D 88 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 101 through 102 removed outlier: 5.521A pdb=" N GLY D 211 " --> pdb=" O GLN D 191 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN D 191 " --> pdb=" O GLY D 211 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS D 213 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER D 189 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS D 215 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL D 187 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 42 through 54 removed outlier: 3.698A pdb=" N GLU E 69 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP E 70 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 126 " --> pdb=" O TRP E 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 54 removed outlier: 3.698A pdb=" N GLU E 69 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 63 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL E 50 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR E 61 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP E 52 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL E 59 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.751A pdb=" N GLY E 207 " --> pdb=" O ARG E 194 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG E 194 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE E 209 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY E 211 " --> pdb=" O VAL E 190 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1677 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: 3.94 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3762 1.34 - 1.46: 2547 1.46 - 1.58: 6429 1.58 - 1.70: 0 1.70 - 1.81: 133 Bond restraints: 12871 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 12866 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.21: 239 105.21 - 112.46: 6999 112.46 - 119.70: 3994 119.70 - 126.95: 6238 126.95 - 134.19: 193 Bond angle restraints: 17663 Sorted by residual: angle pdb=" CA LEU A 235 " pdb=" CB LEU A 235 " pdb=" CG LEU A 235 " ideal model delta sigma weight residual 116.30 126.37 -10.07 3.50e+00 8.16e-02 8.28e+00 angle pdb=" CA LYS C 125 " pdb=" CB LYS C 125 " pdb=" CG LYS C 125 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.52e+00 angle pdb=" N ALA D 28 " pdb=" CA ALA D 28 " pdb=" C ALA D 28 " ideal model delta sigma weight residual 114.56 111.19 3.37 1.27e+00 6.20e-01 7.05e+00 angle pdb=" N ALA A 28 " pdb=" CA ALA A 28 " pdb=" C ALA A 28 " ideal model delta sigma weight residual 114.56 111.26 3.30 1.27e+00 6.20e-01 6.74e+00 angle pdb=" N ALA E 28 " pdb=" CA ALA E 28 " pdb=" C ALA E 28 " ideal model delta sigma weight residual 114.56 111.42 3.14 1.27e+00 6.20e-01 6.13e+00 ... (remaining 17658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.22: 6558 12.22 - 24.44: 607 24.44 - 36.67: 275 36.67 - 48.89: 62 48.89 - 61.11: 27 Dihedral angle restraints: 7529 sinusoidal: 2684 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS E 138 " pdb=" SG CYS E 138 " pdb=" SG CYS E 152 " pdb=" CB CYS E 152 " ideal model delta sinusoidal sigma weight residual 93.00 44.33 48.67 1 1.00e+01 1.00e-02 3.26e+01 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 45.37 47.63 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 45.97 47.03 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 7526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1755 0.057 - 0.115: 380 0.115 - 0.172: 38 0.172 - 0.229: 0 0.229 - 0.287: 1 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE E 180 " pdb=" CA ILE E 180 " pdb=" CG1 ILE E 180 " pdb=" CG2 ILE E 180 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 167 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 167 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2171 not shown) Planarity restraints: 2128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 289 " -0.017 2.00e-02 2.50e+03 1.50e-02 3.96e+00 pdb=" CG PHE A 289 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 289 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 289 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 289 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 78 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO D 79 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 289 " -0.013 2.00e-02 2.50e+03 1.22e-02 2.62e+00 pdb=" CG PHE C 289 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 289 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 289 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 289 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 289 " -0.001 2.00e-02 2.50e+03 ... (remaining 2125 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1637 2.76 - 3.29: 12897 3.29 - 3.83: 21457 3.83 - 4.36: 23388 4.36 - 4.90: 40845 Nonbonded interactions: 100224 Sorted by model distance: nonbonded pdb=" OD1 ASN A 34 " pdb=" OG SER A 36 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASN C 34 " pdb=" OG SER C 36 " model vdw 2.227 2.440 nonbonded pdb=" OD1 ASN D 34 " pdb=" OG SER D 36 " model vdw 2.242 2.440 nonbonded pdb=" OD1 ASN E 34 " pdb=" OG SER E 36 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASN B 34 " pdb=" OG SER B 36 " model vdw 2.247 2.440 ... (remaining 100219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 234 or (resid 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 304 o \ r (resid 305 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 06 through 443 or resid 501)) selection = (chain 'B' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 234 or (resid 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE )) or resid 271 through 306 or (resid 307 and (name N or nam \ e CA or name C or name O or name CB )) or resid 414 through 443 or resid 501)) selection = (chain 'C' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 234 or (resid 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 through 443 or resid 501)) \ selection = chain 'D' selection = (chain 'E' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 234 or (resid 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 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 group one per residue 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: 2.780 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: 9.660 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.910 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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 : 0.003 0.039 12871 Z= 0.230 Angle : 0.718 10.068 17663 Z= 0.385 Chirality : 0.045 0.287 2174 Planarity : 0.004 0.041 2123 Dihedral : 12.692 61.109 4384 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.05 (0.20), residues: 1610 helix: 1.14 (0.23), residues: 530 sheet: -0.52 (0.32), residues: 310 loop : -2.17 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 77 HIS 0.002 0.001 HIS B 68 PHE 0.034 0.002 PHE A 289 TYR 0.024 0.001 TYR D 287 ARG 0.009 0.000 ARG C 171 *********************** 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 377 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8343 (tmm) cc_final: 0.8019 (tpp) REVERT: A 234 PHE cc_start: 0.8842 (t80) cc_final: 0.8579 (t80) REVERT: A 287 TYR cc_start: 0.8255 (t80) cc_final: 0.8022 (t80) REVERT: B 23 HIS cc_start: 0.8676 (t-170) cc_final: 0.8427 (t-170) REVERT: B 129 VAL cc_start: 0.9133 (t) cc_final: 0.8932 (m) REVERT: B 227 MET cc_start: 0.8155 (tmm) cc_final: 0.7893 (tmm) REVERT: B 270 ARG cc_start: 0.7352 (mmt-90) cc_final: 0.7060 (mpt-90) REVERT: B 431 LEU cc_start: 0.8819 (pp) cc_final: 0.8537 (pp) REVERT: C 123 THR cc_start: 0.8432 (p) cc_final: 0.8178 (p) REVERT: C 127 MET cc_start: 0.8220 (mtt) cc_final: 0.7799 (mtm) REVERT: C 197 TRP cc_start: 0.4971 (t-100) cc_final: 0.4694 (t-100) REVERT: C 227 MET cc_start: 0.8478 (tmm) cc_final: 0.8071 (tpp) REVERT: C 431 LEU cc_start: 0.8861 (pp) cc_final: 0.8227 (tp) REVERT: D 77 TRP cc_start: 0.6590 (p-90) cc_final: 0.4841 (p-90) REVERT: D 123 THR cc_start: 0.8450 (p) cc_final: 0.8209 (p) REVERT: D 125 LYS cc_start: 0.8440 (tttm) cc_final: 0.8033 (tmtm) REVERT: D 215 LYS cc_start: 0.8321 (tptp) cc_final: 0.7390 (pttm) REVERT: D 440 TYR cc_start: 0.7731 (t80) cc_final: 0.7439 (t80) REVERT: E 81 ASP cc_start: 0.7087 (p0) cc_final: 0.6409 (t70) REVERT: E 151 MET cc_start: 0.8307 (ttm) cc_final: 0.8012 (ttt) REVERT: E 197 TRP cc_start: 0.5002 (t-100) cc_final: 0.4698 (t-100) REVERT: E 440 TYR cc_start: 0.7476 (t80) cc_final: 0.7098 (t80) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1970 time to fit residues: 112.1205 Evaluate side-chains 278 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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: 0.4980 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12871 Z= 0.219 Angle : 0.674 14.625 17663 Z= 0.330 Chirality : 0.045 0.189 2174 Planarity : 0.004 0.034 2123 Dihedral : 5.020 36.010 1876 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.82 % Allowed : 12.11 % Favored : 86.06 % 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: -1.03 (0.20), residues: 1610 helix: 1.22 (0.22), residues: 530 sheet: -0.36 (0.32), residues: 310 loop : -2.29 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 77 HIS 0.004 0.000 HIS C 161 PHE 0.028 0.002 PHE B 425 TYR 0.020 0.002 TYR A 122 ARG 0.005 0.000 ARG C 171 *********************** 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 336 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 1.669 Fit side-chains REVERT: A 173 GLN cc_start: 0.8305 (pm20) cc_final: 0.7985 (pm20) REVERT: A 227 MET cc_start: 0.8408 (tmm) cc_final: 0.8042 (tpp) REVERT: A 234 PHE cc_start: 0.8941 (t80) cc_final: 0.8597 (t80) REVERT: B 21 ILE cc_start: 0.9115 (tp) cc_final: 0.8459 (tp) REVERT: B 23 HIS cc_start: 0.8679 (t-170) cc_final: 0.8434 (t-170) REVERT: B 129 VAL cc_start: 0.9132 (t) cc_final: 0.8926 (m) REVERT: B 270 ARG cc_start: 0.7306 (mmt-90) cc_final: 0.7086 (mmt-90) REVERT: B 287 TYR cc_start: 0.8498 (t80) cc_final: 0.8133 (t80) REVERT: C 125 LYS cc_start: 0.8060 (tmtt) cc_final: 0.7749 (tmtt) REVERT: C 127 MET cc_start: 0.8201 (mtt) cc_final: 0.7907 (mtm) REVERT: C 197 TRP cc_start: 0.4974 (t-100) cc_final: 0.4718 (t-100) REVERT: D 77 TRP cc_start: 0.6696 (p-90) cc_final: 0.4888 (p-90) REVERT: D 215 LYS cc_start: 0.8459 (tptp) cc_final: 0.7510 (pttt) REVERT: D 440 TYR cc_start: 0.7730 (t80) cc_final: 0.7401 (t80) REVERT: E 81 ASP cc_start: 0.7011 (p0) cc_final: 0.6484 (t70) REVERT: E 197 TRP cc_start: 0.5011 (t-100) cc_final: 0.4719 (t-100) REVERT: E 222 GLN cc_start: 0.8050 (pm20) cc_final: 0.7674 (pm20) REVERT: E 440 TYR cc_start: 0.7594 (t80) cc_final: 0.7200 (t80) outliers start: 23 outliers final: 18 residues processed: 328 average time/residue: 0.2247 time to fit residues: 112.3710 Evaluate side-chains 294 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 145 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 0.0470 chunk 144 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12871 Z= 0.188 Angle : 0.664 14.408 17663 Z= 0.315 Chirality : 0.044 0.150 2174 Planarity : 0.003 0.034 2123 Dihedral : 4.532 25.371 1876 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.74 % Allowed : 17.18 % Favored : 81.08 % 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: -0.97 (0.20), residues: 1610 helix: 1.25 (0.22), residues: 530 sheet: -0.25 (0.32), residues: 310 loop : -2.29 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 PHE 0.028 0.002 PHE B 425 TYR 0.026 0.001 TYR C 220 ARG 0.005 0.000 ARG D 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 326 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 304 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8393 (tmm) cc_final: 0.7973 (tpp) REVERT: A 234 PHE cc_start: 0.8856 (t80) cc_final: 0.8573 (t80) REVERT: B 23 HIS cc_start: 0.8670 (t-170) cc_final: 0.8410 (t-170) REVERT: B 287 TYR cc_start: 0.8450 (t80) cc_final: 0.7968 (t80) REVERT: C 197 TRP cc_start: 0.4912 (t-100) cc_final: 0.4670 (t-100) REVERT: D 77 TRP cc_start: 0.6581 (p-90) cc_final: 0.4773 (p-90) REVERT: D 227 MET cc_start: 0.8422 (tmm) cc_final: 0.8163 (tpp) REVERT: D 440 TYR cc_start: 0.7620 (t80) cc_final: 0.7311 (t80) REVERT: E 197 TRP cc_start: 0.4955 (t-100) cc_final: 0.4690 (t-100) REVERT: E 440 TYR cc_start: 0.7629 (t80) cc_final: 0.7243 (t80) outliers start: 22 outliers final: 19 residues processed: 317 average time/residue: 0.1949 time to fit residues: 94.5450 Evaluate side-chains 290 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 271 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.0970 chunk 109 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.0470 chunk 154 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12871 Z= 0.179 Angle : 0.648 13.430 17663 Z= 0.307 Chirality : 0.043 0.138 2174 Planarity : 0.003 0.029 2123 Dihedral : 4.119 16.019 1876 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.01 % Allowed : 19.64 % Favored : 77.36 % 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: -0.87 (0.20), residues: 1610 helix: 1.28 (0.22), residues: 535 sheet: -0.12 (0.33), residues: 310 loop : -2.25 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 PHE 0.024 0.002 PHE A 425 TYR 0.019 0.001 TYR B 220 ARG 0.004 0.000 ARG B 270 *********************** 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 347 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 309 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8369 (tmm) cc_final: 0.7866 (tpp) REVERT: A 234 PHE cc_start: 0.8804 (t80) cc_final: 0.8522 (t80) REVERT: B 21 ILE cc_start: 0.9140 (tp) cc_final: 0.8633 (tp) REVERT: B 23 HIS cc_start: 0.8672 (t-170) cc_final: 0.8435 (t-170) REVERT: B 287 TYR cc_start: 0.8395 (t80) cc_final: 0.8093 (t80) REVERT: C 197 TRP cc_start: 0.4921 (t-100) cc_final: 0.4439 (t-100) REVERT: C 297 LEU cc_start: 0.8931 (tt) cc_final: 0.8609 (tp) REVERT: D 77 TRP cc_start: 0.6578 (p-90) cc_final: 0.4678 (p-90) REVERT: D 186 GLN cc_start: 0.8130 (pt0) cc_final: 0.7900 (tp40) REVERT: D 215 LYS cc_start: 0.8549 (tptp) cc_final: 0.7689 (pttt) REVERT: D 227 MET cc_start: 0.8493 (tmm) cc_final: 0.8207 (tpp) REVERT: D 241 PHE cc_start: 0.7320 (m-10) cc_final: 0.7112 (m-10) REVERT: D 440 TYR cc_start: 0.7665 (t80) cc_final: 0.7390 (t80) REVERT: E 81 ASP cc_start: 0.6961 (p0) cc_final: 0.6482 (t70) REVERT: E 197 TRP cc_start: 0.5005 (t-100) cc_final: 0.4736 (t-100) REVERT: E 291 MET cc_start: 0.8853 (mmm) cc_final: 0.8380 (mmm) REVERT: E 301 MET cc_start: 0.7762 (mmt) cc_final: 0.7240 (mmm) REVERT: E 440 TYR cc_start: 0.7659 (t80) cc_final: 0.7271 (t80) outliers start: 38 outliers final: 28 residues processed: 333 average time/residue: 0.1883 time to fit residues: 96.7013 Evaluate side-chains 307 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 279 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 151 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE 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: 0.0370 chunk 2 optimal weight: 0.1980 chunk 115 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12871 Z= 0.185 Angle : 0.648 13.389 17663 Z= 0.309 Chirality : 0.043 0.134 2174 Planarity : 0.003 0.028 2123 Dihedral : 4.003 16.838 1876 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.25 % Allowed : 21.46 % Favored : 75.30 % 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: -0.85 (0.20), residues: 1610 helix: 1.30 (0.22), residues: 535 sheet: -0.03 (0.33), residues: 310 loop : -2.27 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 PHE 0.027 0.002 PHE A 425 TYR 0.017 0.001 TYR B 440 ARG 0.003 0.000 ARG B 270 *********************** 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 347 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 306 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8382 (tmm) cc_final: 0.7897 (tpp) REVERT: A 234 PHE cc_start: 0.8750 (t80) cc_final: 0.8525 (t80) REVERT: B 23 HIS cc_start: 0.8658 (t-170) cc_final: 0.8407 (t-170) REVERT: B 231 LEU cc_start: 0.9183 (tt) cc_final: 0.8948 (tt) REVERT: C 104 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.7063 (p0) REVERT: C 125 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7521 (tptt) REVERT: C 127 MET cc_start: 0.8135 (mtt) cc_final: 0.7819 (mtm) REVERT: C 173 GLN cc_start: 0.8112 (pm20) cc_final: 0.7792 (pm20) REVERT: C 197 TRP cc_start: 0.4926 (t-100) cc_final: 0.4691 (t-100) REVERT: C 239 MET cc_start: 0.8103 (ttt) cc_final: 0.7730 (ttt) REVERT: C 291 MET cc_start: 0.8279 (tpp) cc_final: 0.8070 (tpp) REVERT: C 297 LEU cc_start: 0.8970 (tt) cc_final: 0.8611 (tp) REVERT: D 77 TRP cc_start: 0.6597 (p-90) cc_final: 0.4612 (p-90) REVERT: D 186 GLN cc_start: 0.8204 (pt0) cc_final: 0.7942 (tp40) REVERT: D 215 LYS cc_start: 0.8533 (tptp) cc_final: 0.7682 (pttt) REVERT: D 227 MET cc_start: 0.8511 (tmm) cc_final: 0.8230 (tpp) REVERT: D 440 TYR cc_start: 0.7677 (t80) cc_final: 0.7452 (t80) REVERT: E 81 ASP cc_start: 0.6973 (p0) cc_final: 0.6445 (t70) REVERT: E 197 TRP cc_start: 0.5056 (t-100) cc_final: 0.4791 (t-100) REVERT: E 291 MET cc_start: 0.8939 (mmm) cc_final: 0.8714 (mmm) REVERT: E 301 MET cc_start: 0.7767 (mmt) cc_final: 0.7273 (mmm) REVERT: E 440 TYR cc_start: 0.7675 (t80) cc_final: 0.7352 (t80) outliers start: 41 outliers final: 34 residues processed: 327 average time/residue: 0.1959 time to fit residues: 98.5453 Evaluate side-chains 316 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 281 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.0170 chunk 38 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12871 Z= 0.270 Angle : 0.671 13.317 17663 Z= 0.323 Chirality : 0.044 0.139 2174 Planarity : 0.003 0.027 2123 Dihedral : 4.066 15.426 1876 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.56 % Allowed : 21.77 % Favored : 74.66 % 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: -0.79 (0.21), residues: 1610 helix: 1.35 (0.22), residues: 530 sheet: 0.11 (0.31), residues: 330 loop : -2.33 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 77 HIS 0.003 0.000 HIS D 161 PHE 0.033 0.002 PHE A 425 TYR 0.025 0.002 TYR E 287 ARG 0.003 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 341 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 296 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8456 (tmm) cc_final: 0.7977 (tpp) REVERT: A 234 PHE cc_start: 0.8842 (t80) cc_final: 0.8595 (t80) REVERT: B 23 HIS cc_start: 0.8692 (t-170) cc_final: 0.8443 (t-170) REVERT: C 125 LYS cc_start: 0.8191 (tmtt) cc_final: 0.7882 (tptp) REVERT: C 173 GLN cc_start: 0.8136 (pm20) cc_final: 0.7808 (pm20) REVERT: C 197 TRP cc_start: 0.5140 (t-100) cc_final: 0.4908 (t-100) REVERT: D 77 TRP cc_start: 0.6690 (p-90) cc_final: 0.5240 (p-90) REVERT: D 186 GLN cc_start: 0.8301 (pt0) cc_final: 0.8048 (tp40) REVERT: D 215 LYS cc_start: 0.8573 (tptp) cc_final: 0.7839 (pttt) REVERT: D 227 MET cc_start: 0.8497 (tmm) cc_final: 0.8042 (tpp) REVERT: D 241 PHE cc_start: 0.7501 (m-10) cc_final: 0.7297 (m-10) REVERT: D 429 LEU cc_start: 0.8218 (mt) cc_final: 0.7968 (mt) REVERT: D 440 TYR cc_start: 0.7644 (t80) cc_final: 0.7421 (t80) REVERT: E 81 ASP cc_start: 0.6995 (p0) cc_final: 0.6523 (t70) REVERT: E 197 TRP cc_start: 0.5136 (t-100) cc_final: 0.4856 (t-100) REVERT: E 291 MET cc_start: 0.8981 (mmm) cc_final: 0.8345 (tpp) REVERT: E 301 MET cc_start: 0.7743 (mmt) cc_final: 0.7251 (mmm) REVERT: E 440 TYR cc_start: 0.7784 (t80) cc_final: 0.7407 (t80) outliers start: 45 outliers final: 39 residues processed: 323 average time/residue: 0.1935 time to fit residues: 95.4747 Evaluate side-chains 317 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 278 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 277 ASN Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.0030 chunk 17 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 154 optimal weight: 0.0270 chunk 96 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.3248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12871 Z= 0.177 Angle : 0.667 13.342 17663 Z= 0.317 Chirality : 0.044 0.145 2174 Planarity : 0.003 0.028 2123 Dihedral : 3.965 16.387 1876 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.72 % Allowed : 23.59 % Favored : 72.68 % 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: -0.72 (0.21), residues: 1610 helix: 1.36 (0.22), residues: 530 sheet: 0.11 (0.31), residues: 335 loop : -2.24 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 77 HIS 0.003 0.001 HIS D 68 PHE 0.026 0.002 PHE A 425 TYR 0.027 0.001 TYR D 220 ARG 0.002 0.000 ARG B 270 *********************** 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 356 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 309 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8403 (tmm) cc_final: 0.7847 (tpp) REVERT: A 234 PHE cc_start: 0.8797 (t80) cc_final: 0.8553 (t80) REVERT: A 291 MET cc_start: 0.8677 (tpp) cc_final: 0.8429 (tpp) REVERT: B 23 HIS cc_start: 0.8686 (t-170) cc_final: 0.8438 (t-170) REVERT: C 125 LYS cc_start: 0.8078 (tmtt) cc_final: 0.7688 (tptp) REVERT: C 173 GLN cc_start: 0.8150 (pm20) cc_final: 0.7809 (pm20) REVERT: C 197 TRP cc_start: 0.5004 (t-100) cc_final: 0.4769 (t-100) REVERT: C 239 MET cc_start: 0.8146 (ttt) cc_final: 0.7812 (ttt) REVERT: D 77 TRP cc_start: 0.6629 (p-90) cc_final: 0.5243 (p-90) REVERT: D 186 GLN cc_start: 0.8293 (pt0) cc_final: 0.8058 (tp40) REVERT: D 215 LYS cc_start: 0.8548 (tptp) cc_final: 0.7841 (pttt) REVERT: D 227 MET cc_start: 0.8475 (tmm) cc_final: 0.8007 (tpp) REVERT: D 429 LEU cc_start: 0.8142 (mt) cc_final: 0.7898 (mt) REVERT: D 440 TYR cc_start: 0.7673 (t80) cc_final: 0.7440 (t80) REVERT: E 81 ASP cc_start: 0.6947 (p0) cc_final: 0.6641 (t70) REVERT: E 125 LYS cc_start: 0.8343 (tttp) cc_final: 0.7966 (tttp) REVERT: E 197 TRP cc_start: 0.5107 (t-100) cc_final: 0.4848 (t-100) REVERT: E 289 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8419 (t80) REVERT: E 291 MET cc_start: 0.8965 (mmm) cc_final: 0.8462 (tpp) REVERT: E 301 MET cc_start: 0.7774 (mmt) cc_final: 0.7278 (mmm) REVERT: E 440 TYR cc_start: 0.7661 (t80) cc_final: 0.7309 (t80) outliers start: 47 outliers final: 31 residues processed: 331 average time/residue: 0.1995 time to fit residues: 101.1387 Evaluate side-chains 316 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 284 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.0170 chunk 98 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12871 Z= 0.201 Angle : 0.688 14.548 17663 Z= 0.326 Chirality : 0.044 0.141 2174 Planarity : 0.003 0.026 2123 Dihedral : 3.935 20.684 1876 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.09 % Allowed : 25.18 % Favored : 71.73 % 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: -0.70 (0.21), residues: 1610 helix: 1.31 (0.22), residues: 535 sheet: 0.18 (0.31), residues: 335 loop : -2.22 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 PHE 0.027 0.002 PHE A 425 TYR 0.024 0.001 TYR E 287 ARG 0.002 0.000 ARG B 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 327 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 288 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 TRP cc_start: 0.6212 (p-90) cc_final: 0.5010 (p-90) REVERT: A 117 LEU cc_start: 0.8440 (tp) cc_final: 0.8234 (tp) REVERT: A 220 TYR cc_start: 0.8472 (t80) cc_final: 0.8192 (t80) REVERT: B 23 HIS cc_start: 0.8651 (t-170) cc_final: 0.8431 (t-170) REVERT: C 125 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7722 (tptp) REVERT: C 173 GLN cc_start: 0.8199 (pm20) cc_final: 0.7847 (pm20) REVERT: C 197 TRP cc_start: 0.5017 (t-100) cc_final: 0.4792 (t-100) REVERT: C 239 MET cc_start: 0.8180 (ttt) cc_final: 0.7807 (ttt) REVERT: C 291 MET cc_start: 0.8437 (tpp) cc_final: 0.8208 (tpp) REVERT: D 77 TRP cc_start: 0.6677 (p-90) cc_final: 0.5265 (p-90) REVERT: D 127 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7995 (ttm) REVERT: D 186 GLN cc_start: 0.8290 (pt0) cc_final: 0.8063 (tp40) REVERT: D 215 LYS cc_start: 0.8550 (tptp) cc_final: 0.7858 (pttt) REVERT: D 429 LEU cc_start: 0.8189 (mt) cc_final: 0.7929 (mt) REVERT: D 440 TYR cc_start: 0.7693 (t80) cc_final: 0.7413 (t80) REVERT: E 197 TRP cc_start: 0.5141 (t-100) cc_final: 0.4872 (t-100) REVERT: E 220 TYR cc_start: 0.8690 (t80) cc_final: 0.8299 (t80) REVERT: E 289 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8556 (t80) REVERT: E 291 MET cc_start: 0.8992 (mmm) cc_final: 0.8427 (tpp) REVERT: E 301 MET cc_start: 0.7765 (mmt) cc_final: 0.7256 (mmm) REVERT: E 440 TYR cc_start: 0.7665 (t80) cc_final: 0.7341 (t80) outliers start: 39 outliers final: 34 residues processed: 306 average time/residue: 0.1982 time to fit residues: 92.7188 Evaluate side-chains 315 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 279 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12871 Z= 0.208 Angle : 0.690 14.066 17663 Z= 0.328 Chirality : 0.044 0.357 2174 Planarity : 0.003 0.027 2123 Dihedral : 3.912 18.354 1876 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.25 % Allowed : 25.49 % Favored : 71.26 % 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: -0.66 (0.21), residues: 1610 helix: 1.37 (0.22), residues: 535 sheet: 0.17 (0.31), residues: 335 loop : -2.20 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 77 HIS 0.003 0.000 HIS E 68 PHE 0.025 0.002 PHE A 425 TYR 0.020 0.001 TYR E 287 ARG 0.002 0.000 ARG C 171 *********************** 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 324 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 283 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 TRP cc_start: 0.6218 (p-90) cc_final: 0.5037 (p-90) REVERT: A 117 LEU cc_start: 0.8430 (tp) cc_final: 0.8211 (tp) REVERT: B 23 HIS cc_start: 0.8641 (t-170) cc_final: 0.8416 (t-170) REVERT: B 186 GLN cc_start: 0.8148 (tt0) cc_final: 0.7830 (pt0) REVERT: B 440 TYR cc_start: 0.7507 (t80) cc_final: 0.7119 (t80) REVERT: C 125 LYS cc_start: 0.8088 (tmtt) cc_final: 0.7665 (tptp) REVERT: C 173 GLN cc_start: 0.8281 (pm20) cc_final: 0.7938 (pm20) REVERT: C 197 TRP cc_start: 0.5027 (t-100) cc_final: 0.4793 (t-100) REVERT: C 239 MET cc_start: 0.8185 (ttt) cc_final: 0.7813 (ttt) REVERT: D 77 TRP cc_start: 0.6678 (p-90) cc_final: 0.5260 (p-90) REVERT: D 127 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8016 (ttm) REVERT: D 186 GLN cc_start: 0.8313 (pt0) cc_final: 0.8085 (tp40) REVERT: D 215 LYS cc_start: 0.8564 (tptp) cc_final: 0.7869 (pttt) REVERT: D 429 LEU cc_start: 0.8159 (mt) cc_final: 0.7912 (mt) REVERT: D 440 TYR cc_start: 0.7697 (t80) cc_final: 0.7407 (t80) REVERT: E 81 ASP cc_start: 0.7246 (p0) cc_final: 0.6759 (t0) REVERT: E 125 LYS cc_start: 0.8367 (tttp) cc_final: 0.8148 (tttp) REVERT: E 197 TRP cc_start: 0.5161 (t-100) cc_final: 0.4898 (t-100) REVERT: E 220 TYR cc_start: 0.8679 (t80) cc_final: 0.8273 (t80) REVERT: E 289 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8574 (t80) REVERT: E 291 MET cc_start: 0.9009 (mmm) cc_final: 0.8553 (tpp) REVERT: E 301 MET cc_start: 0.7778 (mmt) cc_final: 0.7253 (mmm) REVERT: E 440 TYR cc_start: 0.7622 (t80) cc_final: 0.7297 (t80) outliers start: 41 outliers final: 37 residues processed: 302 average time/residue: 0.1945 time to fit residues: 89.5206 Evaluate side-chains 313 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 274 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0170 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 100 optimal weight: 8.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12871 Z= 0.189 Angle : 0.711 14.607 17663 Z= 0.335 Chirality : 0.044 0.353 2174 Planarity : 0.003 0.026 2123 Dihedral : 3.885 18.836 1876 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.17 % Allowed : 26.13 % Favored : 70.70 % 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: -0.66 (0.21), residues: 1610 helix: 1.33 (0.22), residues: 535 sheet: 0.20 (0.31), residues: 335 loop : -2.18 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 77 HIS 0.003 0.000 HIS D 68 PHE 0.027 0.002 PHE A 425 TYR 0.041 0.002 TYR A 220 ARG 0.002 0.000 ARG B 270 ********************** 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 327 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 287 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8429 (tp) cc_final: 0.8221 (tp) REVERT: B 186 GLN cc_start: 0.8157 (tt0) cc_final: 0.7850 (pt0) REVERT: B 197 TRP cc_start: 0.4857 (t-100) cc_final: 0.4573 (t-100) REVERT: B 440 TYR cc_start: 0.7518 (t80) cc_final: 0.7133 (t80) REVERT: C 173 GLN cc_start: 0.8321 (pm20) cc_final: 0.7975 (pm20) REVERT: C 186 GLN cc_start: 0.8142 (tt0) cc_final: 0.7856 (pt0) REVERT: C 197 TRP cc_start: 0.4979 (t-100) cc_final: 0.4765 (t-100) REVERT: C 239 MET cc_start: 0.8097 (ttt) cc_final: 0.7755 (ttt) REVERT: D 77 TRP cc_start: 0.6670 (p-90) cc_final: 0.4698 (p-90) REVERT: D 127 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8011 (ttm) REVERT: D 186 GLN cc_start: 0.8310 (pt0) cc_final: 0.8090 (tp40) REVERT: D 215 LYS cc_start: 0.8543 (tptp) cc_final: 0.7883 (pttt) REVERT: D 429 LEU cc_start: 0.8188 (mt) cc_final: 0.7939 (mt) REVERT: D 440 TYR cc_start: 0.7720 (t80) cc_final: 0.7433 (t80) REVERT: E 81 ASP cc_start: 0.7231 (p0) cc_final: 0.6722 (t0) REVERT: E 197 TRP cc_start: 0.5133 (t-100) cc_final: 0.4871 (t-100) REVERT: E 220 TYR cc_start: 0.8697 (t80) cc_final: 0.8309 (t80) REVERT: E 289 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8584 (t80) REVERT: E 301 MET cc_start: 0.7777 (mmt) cc_final: 0.7239 (mmm) REVERT: E 440 TYR cc_start: 0.7575 (t80) cc_final: 0.7274 (t80) outliers start: 40 outliers final: 33 residues processed: 306 average time/residue: 0.2015 time to fit residues: 93.5524 Evaluate side-chains 313 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 278 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 130 optimal weight: 0.0770 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 0.2980 chunk 111 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN D 74 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107312 restraints weight = 22532.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110885 restraints weight = 13375.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.113342 restraints weight = 9552.161| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12871 Z= 0.204 Angle : 0.709 13.978 17663 Z= 0.337 Chirality : 0.044 0.337 2174 Planarity : 0.003 0.041 2123 Dihedral : 3.853 18.418 1876 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.93 % Allowed : 27.24 % Favored : 69.83 % 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: -0.64 (0.21), residues: 1610 helix: 1.37 (0.22), residues: 535 sheet: 0.21 (0.31), residues: 335 loop : -2.20 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 77 HIS 0.005 0.001 HIS B 23 PHE 0.034 0.002 PHE D 425 TYR 0.028 0.002 TYR A 220 ARG 0.008 0.000 ARG D 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.18 seconds wall clock time: 51 minutes 43.90 seconds (3103.90 seconds total)