Starting phenix.real_space_refine on Fri Jul 3 06:28:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_16316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_16316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_16316.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_16316.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_16316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_16316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxe_16316/07_2026/8bxe_16316.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'GLU:plan': 8, 'ASP:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} 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: {'GLU:plan': 8, 'ASP:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 2} 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: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} 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: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} 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: {'GLU:plan': 8, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 2} 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 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 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 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 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 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: 3.08, per 1000 atoms: 0.25 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: 1.00 Conformation dependent library (CDL) restraints added in 598.3 milliseconds 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: 0.38 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: 2.07 Time building geometry restraints manager: 1.34 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: 6473 12.22 - 24.44: 597 24.44 - 36.67: 275 36.67 - 48.89: 52 48.89 - 61.11: 27 Dihedral angle restraints: 7424 sinusoidal: 2579 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 7421 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 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 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 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 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: 4.210 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.060 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 12881 Z= 0.165 Angle : 0.718 10.068 17688 Z= 0.385 Chirality : 0.045 0.287 2174 Planarity : 0.004 0.041 2123 Dihedral : 12.654 61.109 4279 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.000 ARG C 171 TYR 0.024 0.001 TYR D 287 PHE 0.034 0.002 PHE A 289 TRP 0.018 0.001 TRP D 77 HIS 0.002 0.001 HIS B 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (12871) covalent geometry : angle 0.71812 / 0.38 (17663) SS BOND : bond 0.00203 / 0.13 ( 5) SS BOND : angle 0.67929 / 0.47 ( 10) hydrogen bonds : bond 0.13527 / 9.87 ( 586) hydrogen bonds : angle 5.95496 / 4.18 ( 1677) link_NAG-ASN : bond 0.00269 / 0.14 ( 5) link_NAG-ASN : angle 0.71803 / 0.48 ( 15) *********************** 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 : 0.416 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: 0.7059 (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: 0.8184 (p) REVERT: C 127 MET cc_start: 0.8221 (mtt) cc_final: 0.7799 (mtm) REVERT: C 197 TRP cc_start: 0.4971 (t-100) cc_final: 0.4695 (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: 0.4843 (p-90) REVERT: D 123 THR cc_start: 0.8451 (p) cc_final: 0.8209 (p) REVERT: D 125 LYS cc_start: 0.8440 (tttm) cc_final: 0.8035 (tmtm) REVERT: D 215 LYS cc_start: 0.8321 (tptp) cc_final: 0.7389 (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: 0.8308 (ttm) cc_final: 0.8011 (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: 0.7099 (t80) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.0903 time to fit residues: 52.5964 Evaluate side-chains 277 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108882 restraints weight = 22466.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.112568 restraints weight = 13002.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115153 restraints weight = 9133.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116945 restraints weight = 7201.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.118079 restraints weight = 6107.560| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12881 Z= 0.138 Angle : 0.703 14.407 17688 Z= 0.340 Chirality : 0.046 0.191 2174 Planarity : 0.004 0.033 2123 Dihedral : 4.306 15.460 1771 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.27 % Allowed : 11.64 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1610 helix: 1.13 (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 ARG 0.004 0.000 ARG C 171 TYR 0.019 0.002 TYR B 122 PHE 0.027 0.002 PHE B 425 TRP 0.011 0.001 TRP A 77 HIS 0.002 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12871) covalent geometry : angle 0.70339 / 0.34 (17663) SS BOND : bond 0.00177 / 0.11 ( 5) SS BOND : angle 0.65361 / 0.45 ( 10) hydrogen bonds : bond 0.04454 / 3.14 ( 586) hydrogen bonds : angle 5.02805 / 3.54 ( 1677) link_NAG-ASN : bond 0.00547 / 0.28 ( 5) link_NAG-ASN : angle 0.44925 / 0.30 ( 15) *********************** 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 344 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 328 time to evaluate : 0.511 Fit side-chains REVERT: A 173 GLN cc_start: 0.8273 (pm20) cc_final: 0.7960 (pm20) REVERT: A 227 MET cc_start: 0.8349 (tmm) cc_final: 0.7858 (tpp) REVERT: A 234 PHE cc_start: 0.8903 (t80) cc_final: 0.8611 (t80) REVERT: B 21 ILE cc_start: 0.9110 (tp) cc_final: 0.8472 (tp) REVERT: B 23 HIS cc_start: 0.8651 (t-170) cc_final: 0.8421 (t-170) REVERT: B 127 MET cc_start: 0.8279 (mtp) cc_final: 0.7991 (ttm) REVERT: B 129 VAL cc_start: 0.9138 (t) cc_final: 0.8938 (m) REVERT: B 173 GLN cc_start: 0.8113 (pm20) cc_final: 0.7450 (pp30) REVERT: B 287 TYR cc_start: 0.8577 (t80) cc_final: 0.8185 (t80) REVERT: C 125 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7698 (tmtt) REVERT: C 127 MET cc_start: 0.8212 (mtt) cc_final: 0.7861 (mtm) REVERT: C 197 TRP cc_start: 0.4753 (t-100) cc_final: 0.4445 (t-100) REVERT: C 222 GLN cc_start: 0.8184 (pm20) cc_final: 0.7639 (pm20) REVERT: D 77 TRP cc_start: 0.6611 (p-90) cc_final: 0.4840 (p-90) REVERT: D 215 LYS cc_start: 0.8496 (tptp) cc_final: 0.7550 (pttt) REVERT: D 440 TYR cc_start: 0.7586 (t80) cc_final: 0.7266 (t80) REVERT: E 197 TRP cc_start: 0.4820 (t-100) cc_final: 0.4529 (t-100) REVERT: E 222 GLN cc_start: 0.8189 (pm20) cc_final: 0.7831 (pm20) REVERT: E 440 TYR cc_start: 0.7466 (t80) cc_final: 0.7074 (t80) outliers start: 16 outliers final: 11 residues processed: 339 average time/residue: 0.0907 time to fit residues: 48.0171 Evaluate side-chains 288 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 277 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 147 optimal weight: 5.9990 chunk 130 optimal weight: 0.2980 chunk 101 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105822 restraints weight = 22687.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109322 restraints weight = 13452.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111809 restraints weight = 9591.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113578 restraints weight = 7612.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114712 restraints weight = 6490.430| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12881 Z= 0.160 Angle : 0.683 12.883 17688 Z= 0.333 Chirality : 0.045 0.155 2174 Planarity : 0.004 0.033 2123 Dihedral : 4.243 15.795 1771 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.82 % Allowed : 16.23 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.20), residues: 1610 helix: 1.17 (0.21), residues: 530 sheet: -0.19 (0.32), residues: 305 loop : -2.25 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 16 TYR 0.026 0.002 TYR C 220 PHE 0.030 0.002 PHE B 425 TRP 0.015 0.001 TRP A 77 HIS 0.001 0.000 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (12871) covalent geometry : angle 0.68362 / 0.33 (17663) SS BOND : bond 0.00196 / 0.11 ( 5) SS BOND : angle 0.65401 / 0.43 ( 10) hydrogen bonds : bond 0.04255 / 2.99 ( 586) hydrogen bonds : angle 4.84786 / 3.44 ( 1677) link_NAG-ASN : bond 0.00349 / 0.18 ( 5) link_NAG-ASN : angle 0.51069 / 0.34 ( 15) *********************** 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 321 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 298 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8214 (pm20) cc_final: 0.7860 (pm20) REVERT: A 227 MET cc_start: 0.8395 (tmm) cc_final: 0.7975 (tpp) REVERT: B 23 HIS cc_start: 0.8693 (t-170) cc_final: 0.8445 (t-170) REVERT: B 129 VAL cc_start: 0.9148 (t) cc_final: 0.8926 (m) REVERT: B 287 TYR cc_start: 0.8613 (t80) cc_final: 0.8082 (t80) REVERT: C 125 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7575 (tptp) REVERT: C 127 MET cc_start: 0.8264 (mtt) cc_final: 0.7882 (mtm) REVERT: C 197 TRP cc_start: 0.4766 (t-100) cc_final: 0.4472 (t-100) REVERT: D 77 TRP cc_start: 0.6611 (p-90) cc_final: 0.4756 (p-90) REVERT: D 123 THR cc_start: 0.8428 (p) cc_final: 0.8158 (p) REVERT: D 227 MET cc_start: 0.8516 (tmm) cc_final: 0.8221 (tpp) REVERT: D 440 TYR cc_start: 0.7548 (t80) cc_final: 0.7288 (t80) REVERT: E 197 TRP cc_start: 0.4888 (t-100) cc_final: 0.4578 (t-100) REVERT: E 222 GLN cc_start: 0.8333 (pm20) cc_final: 0.7950 (mp10) REVERT: E 239 MET cc_start: 0.8174 (ttt) cc_final: 0.7873 (ttt) REVERT: E 440 TYR cc_start: 0.7472 (t80) cc_final: 0.7092 (t80) outliers start: 23 outliers final: 20 residues processed: 312 average time/residue: 0.0852 time to fit residues: 41.5483 Evaluate side-chains 296 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 276 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 147 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 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 D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 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 144 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3648 r_free = 0.3648 target = 0.132982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106990 restraints weight = 22410.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110552 restraints weight = 13201.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.113071 restraints weight = 9351.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114818 restraints weight = 7399.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115966 restraints weight = 6278.844| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12881 Z= 0.137 Angle : 0.672 13.314 17688 Z= 0.324 Chirality : 0.045 0.193 2174 Planarity : 0.003 0.029 2123 Dihedral : 4.139 15.790 1771 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.45 % Allowed : 19.56 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1610 helix: 1.20 (0.21), residues: 535 sheet: -0.18 (0.33), residues: 310 loop : -2.16 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.021 0.001 TYR B 220 PHE 0.026 0.002 PHE B 425 TRP 0.017 0.001 TRP A 77 HIS 0.002 0.000 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12871) covalent geometry : angle 0.67244 / 0.32 (17663) SS BOND : bond 0.00181 / 0.11 ( 5) SS BOND : angle 0.58246 / 0.39 ( 10) hydrogen bonds : bond 0.04059 / 2.84 ( 586) hydrogen bonds : angle 4.75877 / 3.40 ( 1677) link_NAG-ASN : bond 0.00393 / 0.20 ( 5) link_NAG-ASN : angle 0.47652 / 0.33 ( 15) *********************** 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 339 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8115 (tt0) cc_final: 0.7801 (tt0) REVERT: A 227 MET cc_start: 0.8385 (tmm) cc_final: 0.7959 (tpp) REVERT: B 23 HIS cc_start: 0.8672 (t-170) cc_final: 0.8441 (t-170) REVERT: B 129 VAL cc_start: 0.9143 (t) cc_final: 0.8934 (m) REVERT: B 173 GLN cc_start: 0.8077 (pm20) cc_final: 0.7601 (pp30) REVERT: B 270 ARG cc_start: 0.7382 (mmt-90) cc_final: 0.7069 (mpt-90) REVERT: B 287 TYR cc_start: 0.8628 (t80) cc_final: 0.8182 (t80) REVERT: C 125 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7822 (tmtt) REVERT: C 197 TRP cc_start: 0.4723 (t-100) cc_final: 0.4427 (t-100) REVERT: C 222 GLN cc_start: 0.8095 (pm20) cc_final: 0.7754 (pm20) REVERT: C 223 TYR cc_start: 0.8837 (t80) cc_final: 0.8544 (t80) REVERT: D 77 TRP cc_start: 0.6586 (p-90) cc_final: 0.4674 (p-90) REVERT: D 186 GLN cc_start: 0.8109 (pt0) cc_final: 0.7874 (tp40) REVERT: D 215 LYS cc_start: 0.8603 (tptp) cc_final: 0.7766 (pttm) REVERT: D 227 MET cc_start: 0.8527 (tmm) cc_final: 0.8219 (tpp) REVERT: D 440 TYR cc_start: 0.7553 (t80) cc_final: 0.7270 (t80) REVERT: E 197 TRP cc_start: 0.4862 (t-100) cc_final: 0.4526 (t-100) REVERT: E 239 MET cc_start: 0.8188 (ttt) cc_final: 0.7907 (ttt) REVERT: E 291 MET cc_start: 0.8935 (mmm) cc_final: 0.8692 (mmm) REVERT: E 301 MET cc_start: 0.7775 (mmt) cc_final: 0.7157 (mmm) REVERT: E 440 TYR cc_start: 0.7486 (t80) cc_final: 0.7111 (t80) outliers start: 31 outliers final: 26 residues processed: 327 average time/residue: 0.0863 time to fit residues: 44.4568 Evaluate side-chains 301 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 147 PHE 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 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 297 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 74 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 87 optimal weight: 0.0370 chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN E 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107983 restraints weight = 22574.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111406 restraints weight = 13669.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113833 restraints weight = 9860.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115375 restraints weight = 7912.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116623 restraints weight = 6826.270| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12881 Z= 0.124 Angle : 0.681 15.874 17688 Z= 0.324 Chirality : 0.045 0.242 2174 Planarity : 0.003 0.027 2123 Dihedral : 4.109 16.146 1771 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.77 % Allowed : 21.06 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1610 helix: 1.22 (0.21), residues: 535 sheet: -0.08 (0.33), residues: 310 loop : -2.11 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 270 TYR 0.021 0.001 TYR D 223 PHE 0.026 0.002 PHE B 428 TRP 0.020 0.001 TRP A 77 HIS 0.003 0.000 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (12871) covalent geometry : angle 0.68087 / 0.32 (17663) SS BOND : bond 0.00165 / 0.10 ( 5) SS BOND : angle 0.53035 / 0.35 ( 10) hydrogen bonds : bond 0.04006 / 2.81 ( 586) hydrogen bonds : angle 4.69867 / 3.36 ( 1677) link_NAG-ASN : bond 0.00421 / 0.22 ( 5) link_NAG-ASN : angle 0.50902 / 0.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3220 Ramachandran restraints generated. 1610 Oldfield, 0 Emsley, 1610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 312 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8372 (tmm) cc_final: 0.7946 (tpp) REVERT: B 23 HIS cc_start: 0.8673 (t-170) cc_final: 0.8434 (t-170) REVERT: B 129 VAL cc_start: 0.9152 (t) cc_final: 0.8929 (m) REVERT: B 231 LEU cc_start: 0.9196 (tt) cc_final: 0.8970 (tt) REVERT: B 287 TYR cc_start: 0.8574 (t80) cc_final: 0.8292 (t80) REVERT: C 125 LYS cc_start: 0.8100 (tmtt) cc_final: 0.7738 (tptp) REVERT: C 197 TRP cc_start: 0.4680 (t-100) cc_final: 0.4370 (t-100) REVERT: C 222 GLN cc_start: 0.8132 (pm20) cc_final: 0.7780 (mp10) REVERT: C 223 TYR cc_start: 0.8827 (t80) cc_final: 0.8572 (t80) REVERT: C 239 MET cc_start: 0.8147 (ttt) cc_final: 0.7816 (ttt) REVERT: D 77 TRP cc_start: 0.6530 (p-90) cc_final: 0.4632 (p-90) REVERT: D 186 GLN cc_start: 0.8146 (pt0) cc_final: 0.7893 (tp40) REVERT: D 215 LYS cc_start: 0.8576 (tptp) cc_final: 0.7724 (pttm) REVERT: D 220 TYR cc_start: 0.8667 (t80) cc_final: 0.8460 (t80) REVERT: D 227 MET cc_start: 0.8541 (tmm) cc_final: 0.8056 (tpp) REVERT: D 291 MET cc_start: 0.8585 (tpp) cc_final: 0.8378 (tpp) REVERT: D 440 TYR cc_start: 0.7569 (t80) cc_final: 0.7271 (t80) REVERT: E 81 ASP cc_start: 0.7098 (p0) cc_final: 0.6462 (t70) REVERT: E 117 LEU cc_start: 0.8628 (tp) cc_final: 0.8340 (tp) REVERT: E 197 TRP cc_start: 0.4775 (t-100) cc_final: 0.4440 (t-100) REVERT: E 239 MET cc_start: 0.8170 (ttt) cc_final: 0.7871 (ttt) REVERT: E 301 MET cc_start: 0.7795 (mmt) cc_final: 0.7183 (mmm) REVERT: E 440 TYR cc_start: 0.7488 (t80) cc_final: 0.7145 (t80) outliers start: 35 outliers final: 26 residues processed: 334 average time/residue: 0.0832 time to fit residues: 43.5403 Evaluate side-chains 309 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain A residue 155 VAL 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 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 136 optimal weight: 0.0970 chunk 51 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107148 restraints weight = 22209.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110708 restraints weight = 13157.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113232 restraints weight = 9371.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114978 restraints weight = 7442.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116230 restraints weight = 6336.863| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12881 Z= 0.130 Angle : 0.676 15.530 17688 Z= 0.324 Chirality : 0.045 0.244 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.066 16.985 1771 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.61 % Allowed : 22.72 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.20), residues: 1610 helix: 1.30 (0.21), residues: 535 sheet: 0.18 (0.31), residues: 330 loop : -2.07 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.021 0.001 TYR B 220 PHE 0.028 0.002 PHE E 425 TRP 0.023 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (12871) covalent geometry : angle 0.67632 / 0.32 (17663) SS BOND : bond 0.00165 / 0.10 ( 5) SS BOND : angle 0.50008 / 0.33 ( 10) hydrogen bonds : bond 0.03969 / 2.77 ( 586) hydrogen bonds : angle 4.66504 / 3.33 ( 1677) link_NAG-ASN : bond 0.00360 / 0.19 ( 5) link_NAG-ASN : angle 0.53108 / 0.36 ( 15) *********************** 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 334 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 301 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8378 (tmm) cc_final: 0.7995 (tpp) REVERT: A 239 MET cc_start: 0.7962 (ttt) cc_final: 0.7733 (ttt) REVERT: A 431 LEU cc_start: 0.8785 (pp) cc_final: 0.8452 (tp) REVERT: B 23 HIS cc_start: 0.8643 (t-170) cc_final: 0.8432 (t-170) REVERT: B 129 VAL cc_start: 0.9123 (t) cc_final: 0.8900 (m) REVERT: B 270 ARG cc_start: 0.7348 (mmt-90) cc_final: 0.7014 (mpt-90) REVERT: C 125 LYS cc_start: 0.8115 (tmtt) cc_final: 0.7822 (tptp) REVERT: C 127 MET cc_start: 0.8140 (mtt) cc_final: 0.7863 (mtm) REVERT: C 173 GLN cc_start: 0.7957 (pm20) cc_final: 0.7642 (pm20) REVERT: C 197 TRP cc_start: 0.4695 (t-100) cc_final: 0.4395 (t-100) REVERT: C 222 GLN cc_start: 0.8138 (pm20) cc_final: 0.7875 (mp10) REVERT: C 223 TYR cc_start: 0.8823 (t80) cc_final: 0.8608 (t80) REVERT: C 239 MET cc_start: 0.8186 (ttt) cc_final: 0.7801 (ttt) REVERT: D 77 TRP cc_start: 0.6555 (p-90) cc_final: 0.4666 (p-90) REVERT: D 186 GLN cc_start: 0.8148 (pt0) cc_final: 0.7925 (tp40) REVERT: D 215 LYS cc_start: 0.8600 (tptp) cc_final: 0.7824 (pttm) REVERT: D 227 MET cc_start: 0.8539 (tmm) cc_final: 0.8106 (tpp) REVERT: D 241 PHE cc_start: 0.7574 (m-10) cc_final: 0.7268 (m-10) REVERT: D 440 TYR cc_start: 0.7547 (t80) cc_final: 0.7327 (t80) REVERT: E 117 LEU cc_start: 0.8620 (tp) cc_final: 0.8308 (tp) REVERT: E 197 TRP cc_start: 0.4805 (t-100) cc_final: 0.4460 (t-100) REVERT: E 239 MET cc_start: 0.8104 (ttt) cc_final: 0.7818 (ttt) REVERT: E 301 MET cc_start: 0.7770 (mmt) cc_final: 0.7169 (mmm) REVERT: E 440 TYR cc_start: 0.7445 (t80) cc_final: 0.7079 (t80) outliers start: 33 outliers final: 29 residues processed: 318 average time/residue: 0.0863 time to fit residues: 42.7438 Evaluate side-chains 315 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 147 PHE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 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 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 238 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.0020 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106877 restraints weight = 22345.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110582 restraints weight = 13134.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113161 restraints weight = 9312.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114882 restraints weight = 7384.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116154 restraints weight = 6304.831| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12881 Z= 0.126 Angle : 0.687 15.592 17688 Z= 0.328 Chirality : 0.045 0.234 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.036 17.157 1771 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.01 % Allowed : 23.12 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1610 helix: 1.34 (0.21), residues: 535 sheet: 0.24 (0.31), residues: 330 loop : -2.05 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.020 0.001 TYR E 223 PHE 0.023 0.002 PHE A 425 TRP 0.025 0.001 TRP A 77 HIS 0.002 0.000 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12871) covalent geometry : angle 0.68721 / 0.33 (17663) SS BOND : bond 0.00156 / 0.09 ( 5) SS BOND : angle 0.46545 / 0.31 ( 10) hydrogen bonds : bond 0.03938 / 2.75 ( 586) hydrogen bonds : angle 4.64482 / 3.32 ( 1677) link_NAG-ASN : bond 0.00368 / 0.19 ( 5) link_NAG-ASN : angle 0.53154 / 0.36 ( 15) *********************** 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 341 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.8042 (pm20) cc_final: 0.7718 (pm20) REVERT: A 227 MET cc_start: 0.8369 (tmm) cc_final: 0.7929 (tpp) REVERT: A 231 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8836 (tp) REVERT: A 431 LEU cc_start: 0.8809 (pp) cc_final: 0.8485 (tp) REVERT: B 23 HIS cc_start: 0.8701 (t-170) cc_final: 0.8473 (t-170) REVERT: B 129 VAL cc_start: 0.9142 (t) cc_final: 0.8941 (m) REVERT: C 125 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7558 (tptp) REVERT: C 173 GLN cc_start: 0.8037 (pm20) cc_final: 0.7697 (pm20) REVERT: C 197 TRP cc_start: 0.4706 (t-100) cc_final: 0.4405 (t-100) REVERT: C 222 GLN cc_start: 0.8099 (pm20) cc_final: 0.7859 (mp10) REVERT: C 239 MET cc_start: 0.8201 (ttt) cc_final: 0.7838 (ttt) REVERT: D 77 TRP cc_start: 0.6605 (p-90) cc_final: 0.4686 (p-90) REVERT: D 186 GLN cc_start: 0.8200 (pt0) cc_final: 0.7964 (tp40) REVERT: D 215 LYS cc_start: 0.8578 (tptp) cc_final: 0.7814 (pttm) REVERT: D 227 MET cc_start: 0.8497 (tmm) cc_final: 0.8280 (tpp) REVERT: D 241 PHE cc_start: 0.7606 (m-10) cc_final: 0.7308 (m-80) REVERT: D 291 MET cc_start: 0.8545 (tpp) cc_final: 0.8330 (tpp) REVERT: D 440 TYR cc_start: 0.7554 (t80) cc_final: 0.7287 (t80) REVERT: E 173 GLN cc_start: 0.7799 (pm20) cc_final: 0.7378 (tm-30) REVERT: E 197 TRP cc_start: 0.4757 (t-100) cc_final: 0.4421 (t-100) REVERT: E 239 MET cc_start: 0.8108 (ttt) cc_final: 0.7820 (ttt) REVERT: E 289 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.8254 (t80) REVERT: E 301 MET cc_start: 0.7733 (mmt) cc_final: 0.7202 (mmm) REVERT: E 440 TYR cc_start: 0.7451 (t80) cc_final: 0.7137 (t80) outliers start: 38 outliers final: 27 residues processed: 323 average time/residue: 0.0800 time to fit residues: 40.3661 Evaluate side-chains 319 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 290 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 147 PHE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 238 LEU 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 B residue 431 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.133233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106608 restraints weight = 22285.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110093 restraints weight = 13365.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112560 restraints weight = 9616.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114279 restraints weight = 7676.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115358 restraints weight = 6564.772| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12881 Z= 0.133 Angle : 0.698 15.088 17688 Z= 0.336 Chirality : 0.045 0.232 2174 Planarity : 0.003 0.028 2123 Dihedral : 4.016 17.053 1771 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.69 % Allowed : 25.18 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.21), residues: 1610 helix: 1.38 (0.22), residues: 535 sheet: 0.28 (0.31), residues: 330 loop : -2.07 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 270 TYR 0.025 0.001 TYR B 287 PHE 0.030 0.002 PHE C 425 TRP 0.031 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (12871) covalent geometry : angle 0.69827 / 0.34 (17663) SS BOND : bond 0.00158 / 0.09 ( 5) SS BOND : angle 0.48752 / 0.33 ( 10) hydrogen bonds : bond 0.03977 / 2.77 ( 586) hydrogen bonds : angle 4.65350 / 3.33 ( 1677) link_NAG-ASN : bond 0.00314 / 0.16 ( 5) link_NAG-ASN : angle 0.51485 / 0.35 ( 15) *********************** 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 343 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 77 TRP cc_start: 0.6165 (p-90) cc_final: 0.5009 (p-90) REVERT: A 220 TYR cc_start: 0.8506 (t80) cc_final: 0.8300 (t80) REVERT: A 227 MET cc_start: 0.8364 (tmm) cc_final: 0.7961 (tpp) REVERT: A 231 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8830 (tp) REVERT: B 129 VAL cc_start: 0.9118 (t) cc_final: 0.8893 (m) REVERT: B 291 MET cc_start: 0.8593 (tpp) cc_final: 0.8233 (tpp) REVERT: C 125 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7689 (tptp) REVERT: C 173 GLN cc_start: 0.8058 (pm20) cc_final: 0.7737 (pm20) REVERT: C 197 TRP cc_start: 0.4728 (t-100) cc_final: 0.4428 (t-100) REVERT: C 239 MET cc_start: 0.8176 (ttt) cc_final: 0.7795 (ttt) REVERT: D 66 ILE cc_start: 0.9001 (mp) cc_final: 0.8771 (mt) REVERT: D 77 TRP cc_start: 0.6517 (p-90) cc_final: 0.4484 (p-90) REVERT: D 186 GLN cc_start: 0.8218 (pt0) cc_final: 0.8003 (tp40) REVERT: D 215 LYS cc_start: 0.8584 (tptp) cc_final: 0.7843 (pttm) REVERT: D 227 MET cc_start: 0.8465 (tmm) cc_final: 0.8228 (tpp) REVERT: D 291 MET cc_start: 0.8498 (tpp) cc_final: 0.8279 (tpp) REVERT: D 440 TYR cc_start: 0.7543 (t80) cc_final: 0.7284 (t80) REVERT: E 173 GLN cc_start: 0.7853 (pm20) cc_final: 0.7447 (tm-30) REVERT: E 197 TRP cc_start: 0.4773 (t-100) cc_final: 0.4413 (t-100) REVERT: E 239 MET cc_start: 0.8073 (ttt) cc_final: 0.7850 (ttt) REVERT: E 289 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8226 (t80) REVERT: E 301 MET cc_start: 0.7684 (mmt) cc_final: 0.7171 (mmm) REVERT: E 440 TYR cc_start: 0.7454 (t80) cc_final: 0.7106 (t80) outliers start: 34 outliers final: 29 residues processed: 329 average time/residue: 0.0895 time to fit residues: 46.1105 Evaluate side-chains 311 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 147 PHE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 238 LEU 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 224 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 18 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN E 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106109 restraints weight = 22508.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109707 restraints weight = 13284.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112224 restraints weight = 9472.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113826 restraints weight = 7539.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115128 restraints weight = 6487.411| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12881 Z= 0.143 Angle : 0.723 15.891 17688 Z= 0.348 Chirality : 0.046 0.365 2174 Planarity : 0.003 0.028 2123 Dihedral : 4.044 17.347 1771 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.93 % Allowed : 25.42 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.21), residues: 1610 helix: 1.43 (0.22), residues: 535 sheet: 0.29 (0.31), residues: 330 loop : -2.08 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 270 TYR 0.023 0.002 TYR E 223 PHE 0.038 0.002 PHE A 234 TRP 0.025 0.001 TRP A 77 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (12871) covalent geometry : angle 0.72299 / 0.35 (17663) SS BOND : bond 0.00158 / 0.09 ( 5) SS BOND : angle 0.49035 / 0.33 ( 10) hydrogen bonds : bond 0.03996 / 2.78 ( 586) hydrogen bonds : angle 4.69524 / 3.36 ( 1677) link_NAG-ASN : bond 0.00291 / 0.15 ( 5) link_NAG-ASN : angle 0.52914 / 0.36 ( 15) *********************** 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 321 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 284 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 TRP cc_start: 0.6454 (p-90) cc_final: 0.5286 (p-90) REVERT: A 220 TYR cc_start: 0.8466 (t80) cc_final: 0.8178 (t80) REVERT: A 227 MET cc_start: 0.8414 (tmm) cc_final: 0.8009 (tpp) REVERT: A 231 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8851 (tp) REVERT: A 239 MET cc_start: 0.8172 (ttt) cc_final: 0.7864 (ttt) REVERT: A 431 LEU cc_start: 0.8903 (pp) cc_final: 0.8503 (tp) REVERT: B 129 VAL cc_start: 0.9122 (t) cc_final: 0.8920 (m) REVERT: B 291 MET cc_start: 0.8654 (tpp) cc_final: 0.8274 (tpp) REVERT: C 125 LYS cc_start: 0.8076 (tmtt) cc_final: 0.7679 (tptp) REVERT: C 173 GLN cc_start: 0.8116 (pm20) cc_final: 0.7781 (pm20) REVERT: C 197 TRP cc_start: 0.4779 (t-100) cc_final: 0.4473 (t-100) REVERT: C 227 MET cc_start: 0.8508 (tmm) cc_final: 0.8174 (tpp) REVERT: C 239 MET cc_start: 0.8186 (ttt) cc_final: 0.7781 (ttt) REVERT: D 77 TRP cc_start: 0.6585 (p-90) cc_final: 0.4538 (p-90) REVERT: D 186 GLN cc_start: 0.8253 (pt0) cc_final: 0.8046 (tp40) REVERT: D 215 LYS cc_start: 0.8578 (tptp) cc_final: 0.7884 (pttm) REVERT: D 227 MET cc_start: 0.8475 (tmm) cc_final: 0.8250 (tpp) REVERT: D 440 TYR cc_start: 0.7586 (t80) cc_final: 0.7299 (t80) REVERT: E 197 TRP cc_start: 0.4741 (t-100) cc_final: 0.4379 (t-100) REVERT: E 239 MET cc_start: 0.8085 (ttt) cc_final: 0.7813 (ttt) REVERT: E 289 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8257 (t80) REVERT: E 301 MET cc_start: 0.7772 (mmt) cc_final: 0.7201 (mmm) REVERT: E 440 TYR cc_start: 0.7453 (t80) cc_final: 0.7128 (t80) outliers start: 37 outliers final: 32 residues processed: 304 average time/residue: 0.0906 time to fit residues: 43.3181 Evaluate side-chains 308 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 147 PHE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 MET 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 238 LEU Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 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 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 VAL 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 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106222 restraints weight = 22438.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109582 restraints weight = 13856.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111995 restraints weight = 10129.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113584 restraints weight = 8159.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.114650 restraints weight = 7053.188| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12881 Z= 0.138 Angle : 0.736 15.724 17688 Z= 0.351 Chirality : 0.046 0.345 2174 Planarity : 0.003 0.031 2123 Dihedral : 4.112 17.565 1771 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.61 % Allowed : 26.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.21), residues: 1610 helix: 1.37 (0.22), residues: 535 sheet: 0.30 (0.31), residues: 330 loop : -2.09 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.024 0.002 TYR D 220 PHE 0.037 0.002 PHE A 234 TRP 0.025 0.001 TRP A 77 HIS 0.002 0.000 HIS E 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (12871) covalent geometry : angle 0.73644 / 0.35 (17663) SS BOND : bond 0.00151 / 0.08 ( 5) SS BOND : angle 0.48144 / 0.32 ( 10) hydrogen bonds : bond 0.04043 / 2.81 ( 586) hydrogen bonds : angle 4.72380 / 3.38 ( 1677) link_NAG-ASN : bond 0.00293 / 0.15 ( 5) link_NAG-ASN : angle 0.52260 / 0.36 ( 15) ********************** 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 314 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 173 GLN cc_start: 0.7959 (pm20) cc_final: 0.7665 (pm20) REVERT: A 227 MET cc_start: 0.8412 (tmm) cc_final: 0.8040 (tpp) REVERT: A 231 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8836 (tp) REVERT: A 239 MET cc_start: 0.8072 (ttt) cc_final: 0.7742 (ttt) REVERT: B 291 MET cc_start: 0.8582 (tpp) cc_final: 0.8207 (tpp) REVERT: C 125 LYS cc_start: 0.8044 (tmtt) cc_final: 0.7655 (tptp) REVERT: C 173 GLN cc_start: 0.8167 (pm20) cc_final: 0.7841 (pm20) REVERT: C 197 TRP cc_start: 0.4772 (t-100) cc_final: 0.4458 (t-100) REVERT: C 227 MET cc_start: 0.8501 (tmm) cc_final: 0.8193 (tpp) REVERT: D 77 TRP cc_start: 0.6598 (p-90) cc_final: 0.4555 (p-90) REVERT: D 186 GLN cc_start: 0.8302 (pt0) cc_final: 0.8079 (tp40) REVERT: D 215 LYS cc_start: 0.8557 (tptp) cc_final: 0.7860 (pttm) REVERT: D 440 TYR cc_start: 0.7608 (t80) cc_final: 0.7308 (t80) REVERT: E 197 TRP cc_start: 0.4739 (t-100) cc_final: 0.4378 (t-100) REVERT: E 239 MET cc_start: 0.8059 (ttt) cc_final: 0.7790 (ttt) REVERT: E 289 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8282 (t80) REVERT: E 301 MET cc_start: 0.7786 (mmt) cc_final: 0.7310 (mmm) REVERT: E 440 TYR cc_start: 0.7421 (t80) cc_final: 0.7107 (t80) outliers start: 33 outliers final: 28 residues processed: 299 average time/residue: 0.0863 time to fit residues: 40.6701 Evaluate side-chains 301 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 147 PHE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 268 SER 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 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 429 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 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098318 restraints weight = 23034.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101445 restraints weight = 14489.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103623 restraints weight = 10755.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105093 restraints weight = 8799.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106075 restraints weight = 7680.911| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 12881 Z= 0.276 Angle : 0.817 15.530 17688 Z= 0.401 Chirality : 0.050 0.321 2174 Planarity : 0.004 0.031 2123 Dihedral : 4.519 16.980 1771 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.93 % Allowed : 26.44 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.20), residues: 1610 helix: 1.20 (0.21), residues: 530 sheet: 0.12 (0.32), residues: 340 loop : -2.36 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 270 TYR 0.022 0.002 TYR A 220 PHE 0.037 0.003 PHE A 425 TRP 0.029 0.002 TRP A 77 HIS 0.006 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.28 (12871) covalent geometry : angle 0.81667 / 0.40 (17663) SS BOND : bond 0.00297 / 0.14 ( 5) SS BOND : angle 0.74588 / 0.51 ( 10) hydrogen bonds : bond 0.04515 / 3.14 ( 586) hydrogen bonds : angle 5.05874 / 3.62 ( 1677) link_NAG-ASN : bond 0.00197 / 0.10 ( 5) link_NAG-ASN : angle 0.86488 / 0.56 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.16 seconds wall clock time: 38 minutes 36.86 seconds (2316.86 seconds total)