Starting phenix.real_space_refine on Mon Dec 30 08:03:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxe_16316/12_2024/8bxe_16316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxe_16316/12_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/cci-nas-00/data/ceres_data/8bxe_16316/12_2024/8bxe_16316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxe_16316/12_2024/8bxe_16316.map" model { file = "/net/cci-nas-00/data/ceres_data/8bxe_16316/12_2024/8bxe_16316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxe_16316/12_2024/8bxe_16316.cif" } 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. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.96, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 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: 1.23 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: 3.58 Time building geometry restraints manager: 3.72 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: 0.00 - 2.01: 17220 2.01 - 4.03: 379 4.03 - 6.04: 57 6.04 - 8.05: 5 8.05 - 10.07: 2 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 3.040 nonbonded pdb=" OD1 ASN C 34 " pdb=" OG SER C 36 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASN D 34 " pdb=" OG SER D 36 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN E 34 " pdb=" OG SER E 36 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASN B 34 " pdb=" OG SER B 36 " model vdw 2.247 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.990 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.190 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.478 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: 0.2041 time to fit residues: 116.2886 Evaluate side-chains 278 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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: 0.0000 chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 145 optimal weight: 4.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 304 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12871 Z= 0.214 Angle : 0.687 14.014 17663 Z= 0.337 Chirality : 0.046 0.193 2174 Planarity : 0.004 0.033 2123 Dihedral : 5.154 39.577 1876 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.27 % Allowed : 11.48 % Favored : 87.25 % 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: -1.02 (0.20), residues: 1610 helix: 1.14 (0.22), residues: 530 sheet: -0.33 (0.32), residues: 310 loop : -2.24 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 77 HIS 0.002 0.001 HIS C 161 PHE 0.027 0.002 PHE B 425 TYR 0.019 0.002 TYR B 122 ARG 0.005 0.000 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 332 time to evaluate : 1.364 Fit side-chains REVERT: A 173 GLN cc_start: 0.8310 (pm20) cc_final: 0.8009 (pm20) REVERT: A 227 MET cc_start: 0.8388 (tmm) cc_final: 0.8020 (tpp) REVERT: A 234 PHE cc_start: 0.8913 (t80) cc_final: 0.8581 (t80) REVERT: B 21 ILE cc_start: 0.9102 (tp) cc_final: 0.8465 (tp) REVERT: B 23 HIS cc_start: 0.8672 (t-170) cc_final: 0.8435 (t-170) REVERT: B 127 MET cc_start: 0.8303 (mtp) cc_final: 0.8021 (ttm) REVERT: B 173 GLN cc_start: 0.8148 (pm20) cc_final: 0.7465 (pp30) REVERT: B 287 TYR cc_start: 0.8472 (t80) cc_final: 0.8109 (t80) REVERT: C 125 LYS cc_start: 0.8033 (tmtt) cc_final: 0.7726 (tmtt) REVERT: C 127 MET cc_start: 0.8176 (mtt) cc_final: 0.7884 (mtm) REVERT: C 197 TRP cc_start: 0.4780 (t-100) cc_final: 0.4486 (t-100) REVERT: C 222 GLN cc_start: 0.8179 (pm20) cc_final: 0.7784 (pm20) REVERT: D 77 TRP cc_start: 0.6613 (p-90) cc_final: 0.4795 (p-90) REVERT: D 186 GLN cc_start: 0.7313 (mm110) cc_final: 0.7010 (mm-40) REVERT: D 215 LYS cc_start: 0.8458 (tptp) cc_final: 0.7517 (pttt) REVERT: D 220 TYR cc_start: 0.8669 (t80) cc_final: 0.8010 (t80) REVERT: D 440 TYR cc_start: 0.7692 (t80) cc_final: 0.7377 (t80) REVERT: E 81 ASP cc_start: 0.7012 (p0) cc_final: 0.6511 (t70) REVERT: E 197 TRP cc_start: 0.4815 (t-100) cc_final: 0.4529 (t-100) REVERT: E 222 GLN cc_start: 0.8130 (pm20) cc_final: 0.7770 (pm20) REVERT: E 440 TYR cc_start: 0.7579 (t80) cc_final: 0.7213 (t80) outliers start: 16 outliers final: 11 residues processed: 342 average time/residue: 0.2026 time to fit residues: 106.1225 Evaluate side-chains 294 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 283 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL 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 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: 6.9990 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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** D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12871 Z= 0.383 Angle : 0.735 14.441 17663 Z= 0.362 Chirality : 0.047 0.145 2174 Planarity : 0.004 0.033 2123 Dihedral : 4.752 26.924 1876 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.77 % Allowed : 17.50 % Favored : 79.73 % 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: -0.95 (0.20), residues: 1610 helix: 1.17 (0.21), residues: 530 sheet: -0.23 (0.31), residues: 330 loop : -2.25 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 77 HIS 0.004 0.001 HIS C 68 PHE 0.031 0.002 PHE A 425 TYR 0.027 0.002 TYR C 220 ARG 0.004 0.000 ARG B 270 *********************** 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 329 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 294 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8136 (tt0) cc_final: 0.7809 (tt0) REVERT: A 227 MET cc_start: 0.8511 (tmm) cc_final: 0.7986 (tpp) REVERT: A 234 PHE cc_start: 0.8992 (t80) cc_final: 0.8613 (t80) REVERT: A 440 TYR cc_start: 0.7377 (t80) cc_final: 0.7155 (t80) REVERT: B 23 HIS cc_start: 0.8714 (t-170) cc_final: 0.8459 (t-170) REVERT: B 69 GLU cc_start: 0.8102 (tt0) cc_final: 0.7782 (tt0) REVERT: B 287 TYR cc_start: 0.8612 (t80) cc_final: 0.8129 (t80) REVERT: C 123 THR cc_start: 0.8471 (p) cc_final: 0.8266 (p) REVERT: C 125 LYS cc_start: 0.8197 (tmtt) cc_final: 0.7759 (tptp) REVERT: C 127 MET cc_start: 0.8294 (mtt) cc_final: 0.7973 (mtm) REVERT: C 197 TRP cc_start: 0.4984 (t-100) cc_final: 0.4721 (t-100) REVERT: C 227 MET cc_start: 0.8537 (tmm) cc_final: 0.8277 (tpp) REVERT: C 266 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8180 (ttm) REVERT: D 77 TRP cc_start: 0.6699 (p-90) cc_final: 0.5373 (p-90) REVERT: D 123 THR cc_start: 0.8521 (p) cc_final: 0.8276 (p) REVERT: D 125 LYS cc_start: 0.8306 (tttp) cc_final: 0.7624 (tmtm) REVERT: D 127 MET cc_start: 0.8294 (mtt) cc_final: 0.8054 (mtm) REVERT: D 220 TYR cc_start: 0.8716 (t80) cc_final: 0.8038 (t80) REVERT: D 227 MET cc_start: 0.8518 (tmm) cc_final: 0.8272 (tpp) REVERT: D 440 TYR cc_start: 0.7688 (t80) cc_final: 0.7424 (t80) REVERT: E 197 TRP cc_start: 0.5031 (t-100) cc_final: 0.4701 (t-100) REVERT: E 222 GLN cc_start: 0.8322 (pm20) cc_final: 0.8056 (pm20) REVERT: E 239 MET cc_start: 0.8217 (ttt) cc_final: 0.7933 (ttt) REVERT: E 291 MET cc_start: 0.8921 (mmm) cc_final: 0.8687 (mmm) REVERT: E 440 TYR cc_start: 0.7710 (t80) cc_final: 0.7379 (t80) outliers start: 35 outliers final: 29 residues processed: 315 average time/residue: 0.2018 time to fit residues: 97.3778 Evaluate side-chains 289 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 268 SER 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 62 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain D residue 29 ILE 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 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL 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: 0.9980 chunk 109 optimal weight: 0.0570 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 0.0570 overall best weight: 1.0018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2118 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= 0.241 Angle : 0.685 13.350 17663 Z= 0.331 Chirality : 0.045 0.209 2174 Planarity : 0.003 0.028 2123 Dihedral : 4.427 17.347 1876 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.01 % Allowed : 21.38 % Favored : 75.61 % 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: -0.81 (0.20), residues: 1610 helix: 1.28 (0.21), residues: 530 sheet: -0.19 (0.31), residues: 335 loop : -2.14 (0.20), residues: 745 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 0.030 0.002 PHE A 425 TYR 0.022 0.001 TYR D 223 ARG 0.005 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 335 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 297 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8131 (tt0) cc_final: 0.7923 (tt0) REVERT: A 227 MET cc_start: 0.8514 (tmm) cc_final: 0.7963 (tpp) REVERT: A 234 PHE cc_start: 0.8968 (t80) cc_final: 0.8673 (t80) REVERT: A 440 TYR cc_start: 0.7348 (t80) cc_final: 0.7024 (t80) REVERT: B 23 HIS cc_start: 0.8660 (t-170) cc_final: 0.8405 (t-170) REVERT: B 270 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.7195 (mpt-90) REVERT: B 287 TYR cc_start: 0.8561 (t80) cc_final: 0.8119 (t80) REVERT: C 125 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7606 (tptp) REVERT: C 127 MET cc_start: 0.8205 (mtt) cc_final: 0.7885 (mtm) REVERT: C 197 TRP cc_start: 0.4909 (t-100) cc_final: 0.4624 (t-100) REVERT: C 222 GLN cc_start: 0.8175 (pm20) cc_final: 0.7790 (pm20) REVERT: C 223 TYR cc_start: 0.8849 (t80) cc_final: 0.8615 (t80) REVERT: C 227 MET cc_start: 0.8568 (tmm) cc_final: 0.8307 (tpp) REVERT: C 266 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8082 (ttm) REVERT: D 77 TRP cc_start: 0.6669 (p-90) cc_final: 0.5272 (p-90) REVERT: D 125 LYS cc_start: 0.8128 (tttp) cc_final: 0.7431 (tptp) REVERT: D 220 TYR cc_start: 0.8668 (t80) cc_final: 0.7969 (t80) REVERT: D 227 MET cc_start: 0.8495 (tmm) cc_final: 0.8092 (tpp) REVERT: D 440 TYR cc_start: 0.7697 (t80) cc_final: 0.7442 (t80) REVERT: E 197 TRP cc_start: 0.4913 (t-100) cc_final: 0.4574 (t-100) REVERT: E 239 MET cc_start: 0.8229 (ttt) cc_final: 0.7977 (ttt) REVERT: E 291 MET cc_start: 0.8955 (mmm) cc_final: 0.8705 (mmm) REVERT: E 440 TYR cc_start: 0.7649 (t80) cc_final: 0.7311 (t80) outliers start: 38 outliers final: 26 residues processed: 316 average time/residue: 0.2058 time to fit residues: 99.5773 Evaluate side-chains 307 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 224 VAL 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 268 SER Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 266 MET 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 268 SER 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 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 131 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 304 ASN E 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2226 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= 0.229 Angle : 0.681 16.055 17663 Z= 0.328 Chirality : 0.045 0.242 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.239 17.912 1876 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.40 % Allowed : 21.77 % Favored : 74.82 % 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: -0.75 (0.20), residues: 1610 helix: 1.32 (0.21), residues: 530 sheet: -0.12 (0.31), residues: 335 loop : -2.11 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 77 HIS 0.003 0.000 HIS A 68 PHE 0.031 0.002 PHE A 425 TYR 0.024 0.001 TYR D 223 ARG 0.004 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 348 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8175 (tt0) cc_final: 0.7964 (tt0) REVERT: A 173 GLN cc_start: 0.8098 (pm20) cc_final: 0.7780 (pm20) REVERT: A 227 MET cc_start: 0.8528 (tmm) cc_final: 0.7980 (tpp) REVERT: A 234 PHE cc_start: 0.8934 (t80) cc_final: 0.8633 (t80) REVERT: A 440 TYR cc_start: 0.7346 (t80) cc_final: 0.6980 (t80) REVERT: B 23 HIS cc_start: 0.8642 (t-170) cc_final: 0.8402 (t-170) REVERT: B 287 TYR cc_start: 0.8572 (t80) cc_final: 0.8204 (t80) REVERT: C 125 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7789 (tmtt) REVERT: C 127 MET cc_start: 0.8195 (mtt) cc_final: 0.7937 (mtm) REVERT: C 173 GLN cc_start: 0.8213 (pm20) cc_final: 0.7905 (pm20) REVERT: C 197 TRP cc_start: 0.4908 (t-100) cc_final: 0.4623 (t-100) REVERT: C 222 GLN cc_start: 0.8193 (pm20) cc_final: 0.7835 (mp10) REVERT: C 223 TYR cc_start: 0.8862 (t80) cc_final: 0.8611 (t80) REVERT: C 227 MET cc_start: 0.8569 (tmm) cc_final: 0.8173 (tpp) REVERT: D 77 TRP cc_start: 0.6546 (p-90) cc_final: 0.5193 (p-90) REVERT: D 186 GLN cc_start: 0.8259 (pt0) cc_final: 0.8037 (mm-40) REVERT: D 215 LYS cc_start: 0.8648 (tptp) cc_final: 0.7893 (pttm) REVERT: D 220 TYR cc_start: 0.8622 (t80) cc_final: 0.8001 (t80) REVERT: D 227 MET cc_start: 0.8508 (tmm) cc_final: 0.8135 (tpp) REVERT: D 440 TYR cc_start: 0.7713 (t80) cc_final: 0.7452 (t80) REVERT: E 125 LYS cc_start: 0.8479 (tttp) cc_final: 0.8096 (tptp) REVERT: E 197 TRP cc_start: 0.4877 (t-100) cc_final: 0.4538 (t-100) REVERT: E 239 MET cc_start: 0.8164 (ttt) cc_final: 0.7899 (ttt) REVERT: E 289 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8354 (t80) REVERT: E 291 MET cc_start: 0.8965 (mmm) cc_final: 0.8625 (mmm) REVERT: E 301 MET cc_start: 0.7462 (mmt) cc_final: 0.7216 (mmm) REVERT: E 440 TYR cc_start: 0.7690 (t80) cc_final: 0.7336 (t80) outliers start: 43 outliers final: 33 residues processed: 323 average time/residue: 0.1981 time to fit residues: 98.6124 Evaluate side-chains 316 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 MET 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 268 SER 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 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 268 SER 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 170 LEU Chi-restraints excluded: chain D residue 256 LEU 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 151 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.0030 chunk 38 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 128 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- 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 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12871 Z= 0.247 Angle : 0.698 15.606 17663 Z= 0.333 Chirality : 0.045 0.226 2174 Planarity : 0.003 0.025 2123 Dihedral : 4.156 16.503 1876 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.80 % Allowed : 22.57 % Favored : 73.63 % 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: -0.71 (0.20), residues: 1610 helix: 1.33 (0.21), residues: 530 sheet: -0.08 (0.31), residues: 335 loop : -2.08 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 77 HIS 0.003 0.000 HIS A 68 PHE 0.020 0.002 PHE E 425 TYR 0.022 0.001 TYR E 287 ARG 0.005 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 343 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8078 (pm20) cc_final: 0.7736 (pm20) REVERT: A 227 MET cc_start: 0.8514 (tmm) cc_final: 0.7960 (tpp) REVERT: A 234 PHE cc_start: 0.8914 (t80) cc_final: 0.8669 (t80) REVERT: A 440 TYR cc_start: 0.7353 (t80) cc_final: 0.6974 (t80) REVERT: B 23 HIS cc_start: 0.8639 (t-170) cc_final: 0.8389 (t-170) REVERT: B 231 LEU cc_start: 0.9186 (tt) cc_final: 0.8977 (tt) REVERT: B 270 ARG cc_start: 0.7351 (mmt-90) cc_final: 0.7134 (mpt-90) REVERT: B 287 TYR cc_start: 0.8530 (t80) cc_final: 0.8167 (t80) REVERT: C 125 LYS cc_start: 0.8109 (tmtt) cc_final: 0.7624 (tptp) REVERT: C 127 MET cc_start: 0.8174 (mtt) cc_final: 0.7822 (mtm) REVERT: C 173 GLN cc_start: 0.8213 (pm20) cc_final: 0.7895 (pm20) REVERT: C 197 TRP cc_start: 0.4912 (t-100) cc_final: 0.4647 (t-100) REVERT: C 222 GLN cc_start: 0.8225 (pm20) cc_final: 0.7937 (mp10) REVERT: C 227 MET cc_start: 0.8583 (tmm) cc_final: 0.8195 (tpp) REVERT: D 77 TRP cc_start: 0.6566 (p-90) cc_final: 0.5211 (p-90) REVERT: D 215 LYS cc_start: 0.8643 (tptp) cc_final: 0.7906 (pttm) REVERT: D 220 TYR cc_start: 0.8627 (t80) cc_final: 0.7979 (t80) REVERT: D 227 MET cc_start: 0.8491 (tmm) cc_final: 0.8156 (tpp) REVERT: D 440 TYR cc_start: 0.7703 (t80) cc_final: 0.7433 (t80) REVERT: E 81 ASP cc_start: 0.7203 (p0) cc_final: 0.6688 (t70) REVERT: E 125 LYS cc_start: 0.8463 (tttp) cc_final: 0.7895 (tptp) REVERT: E 197 TRP cc_start: 0.4960 (t-100) cc_final: 0.4619 (t-100) REVERT: E 220 TYR cc_start: 0.8834 (t80) cc_final: 0.8519 (t80) REVERT: E 239 MET cc_start: 0.8159 (ttt) cc_final: 0.7886 (ttt) REVERT: E 289 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8492 (t80) REVERT: E 291 MET cc_start: 0.8988 (mmm) cc_final: 0.8593 (mmm) REVERT: E 440 TYR cc_start: 0.7727 (t80) cc_final: 0.7361 (t80) outliers start: 48 outliers final: 38 residues processed: 322 average time/residue: 0.2025 time to fit residues: 99.6900 Evaluate side-chains 316 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 278 VAL 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 268 SER 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 155 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 268 SER 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 170 LEU Chi-restraints excluded: chain D residue 268 SER 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 50 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.0670 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12871 Z= 0.210 Angle : 0.686 15.866 17663 Z= 0.329 Chirality : 0.045 0.228 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.091 16.914 1876 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.12 % Allowed : 23.83 % Favored : 72.05 % 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: -0.67 (0.20), residues: 1610 helix: 1.36 (0.22), residues: 530 sheet: -0.02 (0.31), residues: 335 loop : -2.07 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 77 HIS 0.004 0.001 HIS A 68 PHE 0.015 0.002 PHE C 145 TYR 0.023 0.001 TYR A 220 ARG 0.004 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 349 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8698 (tmtt) cc_final: 0.8411 (tmtt) REVERT: A 173 GLN cc_start: 0.8100 (pm20) cc_final: 0.7764 (pm20) REVERT: A 227 MET cc_start: 0.8487 (tmm) cc_final: 0.7926 (tpp) REVERT: A 234 PHE cc_start: 0.8895 (t80) cc_final: 0.8689 (t80) REVERT: A 440 TYR cc_start: 0.7356 (t80) cc_final: 0.6962 (t80) REVERT: B 23 HIS cc_start: 0.8620 (t-170) cc_final: 0.8379 (t-170) REVERT: B 227 MET cc_start: 0.8500 (tmm) cc_final: 0.8008 (tmm) REVERT: C 125 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7724 (tptp) REVERT: C 173 GLN cc_start: 0.8243 (pm20) cc_final: 0.7919 (pm20) REVERT: C 197 TRP cc_start: 0.4883 (t-100) cc_final: 0.4615 (t-100) REVERT: C 222 GLN cc_start: 0.8158 (pm20) cc_final: 0.7943 (mp10) REVERT: C 227 MET cc_start: 0.8583 (tmm) cc_final: 0.8199 (tpp) REVERT: D 77 TRP cc_start: 0.6549 (p-90) cc_final: 0.5170 (p-90) REVERT: D 186 GLN cc_start: 0.7693 (mm110) cc_final: 0.7477 (tp40) REVERT: D 215 LYS cc_start: 0.8588 (tptp) cc_final: 0.7894 (pttt) REVERT: D 220 TYR cc_start: 0.8630 (t80) cc_final: 0.7987 (t80) REVERT: D 440 TYR cc_start: 0.7689 (t80) cc_final: 0.7385 (t80) REVERT: E 125 LYS cc_start: 0.8408 (tttp) cc_final: 0.7888 (tptp) REVERT: E 197 TRP cc_start: 0.4886 (t-100) cc_final: 0.4556 (t-100) REVERT: E 220 TYR cc_start: 0.8792 (t80) cc_final: 0.8398 (t80) REVERT: E 289 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8506 (t80) REVERT: E 291 MET cc_start: 0.8996 (mmm) cc_final: 0.8573 (mmm) REVERT: E 440 TYR cc_start: 0.7626 (t80) cc_final: 0.7331 (t80) outliers start: 52 outliers final: 40 residues processed: 327 average time/residue: 0.2169 time to fit residues: 108.2901 Evaluate side-chains 323 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL 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 268 SER 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 155 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 SER 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 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER 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 50 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 98 optimal weight: 0.0040 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12871 Z= 0.253 Angle : 0.712 15.683 17663 Z= 0.344 Chirality : 0.046 0.342 2174 Planarity : 0.003 0.027 2123 Dihedral : 4.075 17.105 1876 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.96 % Allowed : 24.86 % Favored : 71.18 % 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: -0.68 (0.21), residues: 1610 helix: 1.35 (0.21), residues: 530 sheet: 0.09 (0.31), residues: 330 loop : -2.13 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 77 HIS 0.003 0.001 HIS E 68 PHE 0.015 0.002 PHE C 425 TYR 0.023 0.002 TYR E 287 ARG 0.006 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 344 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8500 (tmtt) REVERT: A 173 GLN cc_start: 0.8089 (pm20) cc_final: 0.7740 (pm20) REVERT: A 227 MET cc_start: 0.8487 (tmm) cc_final: 0.7929 (tpp) REVERT: A 234 PHE cc_start: 0.8896 (t80) cc_final: 0.8695 (t80) REVERT: A 440 TYR cc_start: 0.7398 (t80) cc_final: 0.7002 (t80) REVERT: B 127 MET cc_start: 0.8333 (ttm) cc_final: 0.8065 (ttm) REVERT: C 125 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7770 (tptp) REVERT: C 173 GLN cc_start: 0.8213 (pm20) cc_final: 0.7903 (pm20) REVERT: C 197 TRP cc_start: 0.4985 (t-100) cc_final: 0.4712 (t-100) REVERT: C 227 MET cc_start: 0.8597 (tmm) cc_final: 0.8263 (tpp) REVERT: D 77 TRP cc_start: 0.6596 (p-90) cc_final: 0.5224 (p-90) REVERT: D 186 GLN cc_start: 0.7683 (mm110) cc_final: 0.7416 (tp40) REVERT: D 215 LYS cc_start: 0.8617 (tptp) cc_final: 0.7903 (pttt) REVERT: D 220 TYR cc_start: 0.8646 (t80) cc_final: 0.8026 (t80) REVERT: D 440 TYR cc_start: 0.7749 (t80) cc_final: 0.7445 (t80) REVERT: E 197 TRP cc_start: 0.4939 (t-100) cc_final: 0.4594 (t-100) REVERT: E 220 TYR cc_start: 0.8782 (t80) cc_final: 0.8393 (t80) REVERT: E 227 MET cc_start: 0.8593 (tmm) cc_final: 0.8064 (tpp) REVERT: E 289 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8547 (t80) REVERT: E 291 MET cc_start: 0.8999 (mmm) cc_final: 0.8585 (mmm) REVERT: E 301 MET cc_start: 0.7469 (mmt) cc_final: 0.7214 (mmm) REVERT: E 440 TYR cc_start: 0.7620 (t80) cc_final: 0.7343 (t80) outliers start: 50 outliers final: 42 residues processed: 323 average time/residue: 0.2153 time to fit residues: 107.3284 Evaluate side-chains 319 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR 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 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 155 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 SER 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 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER 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 50 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 TYR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU 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: 0.8980 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12871 Z= 0.235 Angle : 0.717 15.477 17663 Z= 0.344 Chirality : 0.046 0.318 2174 Planarity : 0.003 0.033 2123 Dihedral : 4.095 17.364 1876 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.48 % Allowed : 26.37 % Favored : 70.15 % 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: -0.67 (0.21), residues: 1610 helix: 1.34 (0.22), residues: 530 sheet: 0.04 (0.31), residues: 335 loop : -2.09 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 77 HIS 0.003 0.000 HIS E 68 PHE 0.015 0.002 PHE C 145 TYR 0.021 0.002 TYR E 287 ARG 0.005 0.000 ARG B 270 *********************** 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 338 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8190 (tt0) cc_final: 0.7984 (tt0) REVERT: A 155 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8291 (p) REVERT: A 173 GLN cc_start: 0.8077 (pm20) cc_final: 0.7762 (pm20) REVERT: A 227 MET cc_start: 0.8474 (tmm) cc_final: 0.7912 (tpp) REVERT: A 234 PHE cc_start: 0.8872 (t80) cc_final: 0.8575 (t80) REVERT: B 21 ILE cc_start: 0.9109 (tp) cc_final: 0.8909 (tp) REVERT: B 287 TYR cc_start: 0.8522 (t80) cc_final: 0.8126 (t80) REVERT: B 440 TYR cc_start: 0.7495 (t80) cc_final: 0.7119 (t80) REVERT: C 125 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7732 (tptp) REVERT: C 173 GLN cc_start: 0.8267 (pm20) cc_final: 0.7970 (pm20) REVERT: C 197 TRP cc_start: 0.4933 (t-100) cc_final: 0.4656 (t-100) REVERT: C 227 MET cc_start: 0.8625 (tmm) cc_final: 0.8318 (tpp) REVERT: D 77 TRP cc_start: 0.6584 (p-90) cc_final: 0.5234 (p-90) REVERT: D 186 GLN cc_start: 0.7698 (mm110) cc_final: 0.7423 (tp40) REVERT: D 215 LYS cc_start: 0.8604 (tptp) cc_final: 0.7910 (pttt) REVERT: D 220 TYR cc_start: 0.8644 (t80) cc_final: 0.8104 (t80) REVERT: D 429 LEU cc_start: 0.8295 (mt) cc_final: 0.8042 (mt) REVERT: D 440 TYR cc_start: 0.7752 (t80) cc_final: 0.7450 (t80) REVERT: E 117 LEU cc_start: 0.8618 (tp) cc_final: 0.8325 (tp) REVERT: E 125 LYS cc_start: 0.8391 (tttp) cc_final: 0.7929 (tptp) REVERT: E 197 TRP cc_start: 0.4915 (t-100) cc_final: 0.4570 (t-100) REVERT: E 220 TYR cc_start: 0.8808 (t80) cc_final: 0.8547 (t80) REVERT: E 227 MET cc_start: 0.8657 (tmm) cc_final: 0.8236 (tpp) REVERT: E 289 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8535 (t80) REVERT: E 291 MET cc_start: 0.8974 (mmm) cc_final: 0.8591 (mmm) REVERT: E 301 MET cc_start: 0.7469 (mmt) cc_final: 0.7202 (mmm) REVERT: E 440 TYR cc_start: 0.7535 (t80) cc_final: 0.7252 (t80) outliers start: 44 outliers final: 40 residues processed: 324 average time/residue: 0.2006 time to fit residues: 99.5002 Evaluate side-chains 325 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 283 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR 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 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 155 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 17 LEU 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 88 ILE Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER 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 50 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 98 optimal weight: 0.0170 chunk 77 optimal weight: 0.4980 chunk 100 optimal weight: 0.1980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12871 Z= 0.199 Angle : 0.736 17.119 17663 Z= 0.352 Chirality : 0.046 0.310 2174 Planarity : 0.003 0.031 2123 Dihedral : 4.100 17.683 1876 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.09 % Allowed : 27.24 % Favored : 69.68 % 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: -0.64 (0.21), residues: 1610 helix: 1.26 (0.22), residues: 535 sheet: 0.13 (0.31), residues: 335 loop : -2.05 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 77 HIS 0.003 0.000 HIS D 68 PHE 0.019 0.002 PHE A 241 TYR 0.020 0.002 TYR A 220 ARG 0.005 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 340 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 301 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8661 (tmtt) cc_final: 0.8286 (tmtt) REVERT: A 155 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8321 (p) REVERT: A 173 GLN cc_start: 0.8084 (pm20) cc_final: 0.7767 (pm20) REVERT: A 234 PHE cc_start: 0.8842 (t80) cc_final: 0.8562 (t80) REVERT: B 287 TYR cc_start: 0.8446 (t80) cc_final: 0.8112 (t80) REVERT: B 440 TYR cc_start: 0.7453 (t80) cc_final: 0.7102 (t80) REVERT: C 125 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7680 (tptp) REVERT: C 173 GLN cc_start: 0.8299 (pm20) cc_final: 0.8020 (pm20) REVERT: C 197 TRP cc_start: 0.4850 (t-100) cc_final: 0.4562 (t-100) REVERT: C 227 MET cc_start: 0.8656 (tmm) cc_final: 0.8391 (tpp) REVERT: C 265 MET cc_start: 0.8464 (ttt) cc_final: 0.8123 (ttm) REVERT: D 77 TRP cc_start: 0.6565 (p-90) cc_final: 0.5204 (p-90) REVERT: D 186 GLN cc_start: 0.7737 (mm110) cc_final: 0.7453 (tp40) REVERT: D 215 LYS cc_start: 0.8594 (tptp) cc_final: 0.7901 (pttt) REVERT: D 220 TYR cc_start: 0.8618 (t80) cc_final: 0.8183 (t80) REVERT: D 291 MET cc_start: 0.8533 (tpp) cc_final: 0.8134 (tpp) REVERT: D 429 LEU cc_start: 0.8273 (mt) cc_final: 0.7997 (mt) REVERT: D 440 TYR cc_start: 0.7777 (t80) cc_final: 0.7467 (t80) REVERT: E 117 LEU cc_start: 0.8604 (tp) cc_final: 0.8316 (tp) REVERT: E 197 TRP cc_start: 0.4810 (t-100) cc_final: 0.4465 (t-100) REVERT: E 220 TYR cc_start: 0.8803 (t80) cc_final: 0.8514 (t80) REVERT: E 227 MET cc_start: 0.8698 (tmm) cc_final: 0.8320 (tpp) REVERT: E 289 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.8515 (t80) REVERT: E 291 MET cc_start: 0.8969 (mmm) cc_final: 0.8648 (mmm) REVERT: E 301 MET cc_start: 0.7440 (mmt) cc_final: 0.7218 (mmm) REVERT: E 440 TYR cc_start: 0.7506 (t80) cc_final: 0.7242 (t80) outliers start: 39 outliers final: 34 residues processed: 329 average time/residue: 0.2066 time to fit residues: 103.6782 Evaluate side-chains 324 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL 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 224 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR 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 B residue 304 ASN 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 155 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 SER 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 112 TYR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER 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 50 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 289 PHE Chi-restraints excluded: chain E residue 297 LEU 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: 0.5980 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.104311 restraints weight = 22425.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107706 restraints weight = 13475.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110153 restraints weight = 9708.601| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12871 Z= 0.219 Angle : 0.753 17.028 17663 Z= 0.356 Chirality : 0.047 0.368 2174 Planarity : 0.003 0.036 2123 Dihedral : 4.067 17.896 1876 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.93 % Allowed : 28.03 % Favored : 69.04 % 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: -0.67 (0.21), residues: 1610 helix: 1.20 (0.21), residues: 535 sheet: 0.22 (0.31), residues: 330 loop : -2.08 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 77 HIS 0.003 0.000 HIS D 68 PHE 0.037 0.002 PHE E 425 TYR 0.019 0.002 TYR A 440 ARG 0.005 0.000 ARG B 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2798.55 seconds wall clock time: 51 minutes 57.08 seconds (3117.08 seconds total)