Starting phenix.real_space_refine on Sat Aug 23 14:14:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bxe_16316/08_2025/8bxe_16316.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bxe_16316/08_2025/8bxe_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_16316/08_2025/8bxe_16316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bxe_16316/08_2025/8bxe_16316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bxe_16316/08_2025/8bxe_16316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bxe_16316/08_2025/8bxe_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.33, per 1000 atoms: 0.19 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: 0.96 Conformation dependent library (CDL) restraints added in 444.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.43 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: 1.41 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3762 1.34 - 1.46: 2547 1.46 - 1.58: 6429 1.58 - 1.70: 0 1.70 - 1.81: 133 Bond restraints: 12871 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 ... (remaining 12866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17220 2.01 - 4.03: 379 4.03 - 6.04: 57 6.04 - 8.05: 5 8.05 - 10.07: 2 Bond angle restraints: 17663 Sorted by residual: angle pdb=" CA LEU A 235 " pdb=" CB LEU A 235 " pdb=" CG LEU A 235 " ideal model delta sigma weight residual 116.30 126.37 -10.07 3.50e+00 8.16e-02 8.28e+00 angle pdb=" CA LYS C 125 " pdb=" CB LYS C 125 " pdb=" CG LYS C 125 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.52e+00 angle pdb=" N ALA D 28 " pdb=" CA ALA D 28 " pdb=" C ALA D 28 " ideal model delta sigma weight residual 114.56 111.19 3.37 1.27e+00 6.20e-01 7.05e+00 angle pdb=" N ALA A 28 " pdb=" CA ALA A 28 " pdb=" C ALA A 28 " ideal model delta sigma weight residual 114.56 111.26 3.30 1.27e+00 6.20e-01 6.74e+00 angle pdb=" N ALA E 28 " pdb=" CA ALA E 28 " pdb=" C ALA E 28 " ideal model delta sigma weight residual 114.56 111.42 3.14 1.27e+00 6.20e-01 6.13e+00 ... (remaining 17658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.22: 6558 12.22 - 24.44: 607 24.44 - 36.67: 275 36.67 - 48.89: 62 48.89 - 61.11: 27 Dihedral angle restraints: 7529 sinusoidal: 2684 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS E 138 " pdb=" SG CYS E 138 " pdb=" SG CYS E 152 " pdb=" CB CYS E 152 " ideal model delta sinusoidal sigma weight residual 93.00 44.33 48.67 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 45.37 47.63 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 45.97 47.03 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 7526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1755 0.057 - 0.115: 380 0.115 - 0.172: 38 0.172 - 0.229: 0 0.229 - 0.287: 1 Chirality restraints: 2174 Sorted by residual: chirality pdb=" CB ILE E 180 " pdb=" CA ILE E 180 " pdb=" CG1 ILE E 180 " pdb=" CG2 ILE E 180 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 167 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 167 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2171 not shown) Planarity restraints: 2128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 289 " -0.017 2.00e-02 2.50e+03 1.50e-02 3.96e+00 pdb=" CG PHE A 289 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 289 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 289 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 289 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 78 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO D 79 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 79 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 79 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 289 " -0.013 2.00e-02 2.50e+03 1.22e-02 2.62e+00 pdb=" CG PHE C 289 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 289 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 289 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 289 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 289 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 289 " -0.001 2.00e-02 2.50e+03 ... (remaining 2125 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1637 2.76 - 3.29: 12897 3.29 - 3.83: 21457 3.83 - 4.36: 23388 4.36 - 4.90: 40845 Nonbonded interactions: 100224 Sorted by model distance: nonbonded pdb=" OD1 ASN A 34 " pdb=" OG SER A 36 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN C 34 " pdb=" OG SER C 36 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASN D 34 " pdb=" OG SER D 36 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN E 34 " pdb=" OG SER E 36 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASN B 34 " pdb=" OG SER B 36 " model vdw 2.247 3.040 ... (remaining 100219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 23 or (resid 24 and (name N or nam \ e CA or name C or name O or name CB )) or resid 25 through 234 or (resid 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 304 o \ r (resid 305 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 06 through 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: 2.240 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.950 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 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 : 12.692 61.109 4384 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00346 (12871) covalent geometry : angle 0.71812 (17663) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.67929 ( 10) hydrogen bonds : bond 0.13527 ( 586) hydrogen bonds : angle 5.95496 ( 1677) link_NAG-ASN : bond 0.00269 ( 5) link_NAG-ASN : angle 0.71803 ( 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 : 0.413 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: 0.8220 (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: 0.8450 (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: 0.8307 (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: 0.0801 time to fit residues: 46.7288 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 : 0.381 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN ** 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 = 0.3680 r_free = 0.3680 target = 0.134728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108615 restraints weight = 22475.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112294 restraints weight = 12964.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114846 restraints weight = 9090.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116673 restraints weight = 7164.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117647 restraints weight = 6069.949| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1407 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= 0.142 Angle : 0.706 14.701 17688 Z= 0.342 Chirality : 0.046 0.194 2174 Planarity : 0.004 0.033 2123 Dihedral : 5.159 39.490 1876 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.35 % Allowed : 11.64 % Favored : 87.02 % 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 aren 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 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00310 (12871) covalent geometry : angle 0.70661 (17663) SS BOND : bond 0.00172 ( 5) SS BOND : angle 0.65291 ( 10) hydrogen bonds : bond 0.04382 ( 586) hydrogen bonds : angle 5.01414 ( 1677) link_NAG-ASN : bond 0.00436 ( 5) link_NAG-ASN : angle 0.46778 ( 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 347 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 330 time to evaluate : 0.298 Fit side-chains REVERT: A 117 LEU cc_start: 0.8583 (tp) cc_final: 0.8293 (tp) REVERT: A 173 GLN cc_start: 0.8284 (pm20) cc_final: 0.7976 (pm20) REVERT: A 227 MET cc_start: 0.8350 (tmm) cc_final: 0.7957 (tpp) REVERT: A 234 PHE cc_start: 0.8899 (t80) cc_final: 0.8550 (t80) REVERT: B 21 ILE cc_start: 0.9118 (tp) cc_final: 0.8476 (tp) REVERT: B 23 HIS cc_start: 0.8647 (t-170) cc_final: 0.8416 (t-170) REVERT: B 127 MET cc_start: 0.8277 (mtp) cc_final: 0.7991 (ttm) REVERT: B 129 VAL cc_start: 0.9135 (t) cc_final: 0.8934 (m) REVERT: B 173 GLN cc_start: 0.8112 (pm20) cc_final: 0.7447 (pp30) REVERT: B 287 TYR cc_start: 0.8575 (t80) cc_final: 0.8185 (t80) REVERT: C 125 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7568 (tptp) REVERT: C 127 MET cc_start: 0.8208 (mtt) cc_final: 0.7802 (mtm) REVERT: C 197 TRP cc_start: 0.4743 (t-100) cc_final: 0.4439 (t-100) REVERT: C 222 GLN cc_start: 0.8166 (pm20) cc_final: 0.7620 (pm20) REVERT: D 77 TRP cc_start: 0.6611 (p-90) cc_final: 0.4837 (p-90) REVERT: D 215 LYS cc_start: 0.8498 (tptp) cc_final: 0.7550 (pttt) REVERT: D 220 TYR cc_start: 0.8702 (t80) cc_final: 0.7987 (t80) REVERT: D 440 TYR cc_start: 0.7607 (t80) cc_final: 0.7277 (t80) REVERT: E 197 TRP cc_start: 0.4837 (t-100) cc_final: 0.4545 (t-100) REVERT: E 222 GLN cc_start: 0.8186 (pm20) cc_final: 0.7814 (pm20) REVERT: E 440 TYR cc_start: 0.7479 (t80) cc_final: 0.7071 (t80) outliers start: 17 outliers final: 12 residues processed: 342 average time/residue: 0.0763 time to fit residues: 40.6512 Evaluate side-chains 292 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 280 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 268 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 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: 5.9990 chunk 101 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 126 optimal weight: 0.0470 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105572 restraints weight = 22732.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.109118 restraints weight = 13411.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111582 restraints weight = 9505.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.113329 restraints weight = 7537.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114452 restraints weight = 6402.431| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1726 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= 0.159 Angle : 0.679 12.755 17688 Z= 0.331 Chirality : 0.045 0.148 2174 Planarity : 0.004 0.032 2123 Dihedral : 4.629 27.543 1876 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.66 % Allowed : 17.02 % Favored : 81.31 % 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 aren not related in a simple way. whole: -0.95 (0.20), residues: 1610 helix: 1.21 (0.21), residues: 530 sheet: -0.18 (0.32), residues: 305 loop : -2.23 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 16 TYR 0.026 0.001 TYR C 220 PHE 0.029 0.002 PHE B 425 TRP 0.014 0.001 TRP A 77 HIS 0.001 0.000 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00370 (12871) covalent geometry : angle 0.67856 (17663) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.65520 ( 10) hydrogen bonds : bond 0.04229 ( 586) hydrogen bonds : angle 4.81639 ( 1677) link_NAG-ASN : bond 0.00284 ( 5) link_NAG-ASN : angle 0.61887 ( 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 318 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8398 (tmm) cc_final: 0.7980 (tpp) REVERT: B 23 HIS cc_start: 0.8687 (t-170) cc_final: 0.8441 (t-170) REVERT: B 129 VAL cc_start: 0.9159 (t) cc_final: 0.8933 (m) REVERT: B 173 GLN cc_start: 0.8163 (pm20) cc_final: 0.7641 (pp30) REVERT: B 287 TYR cc_start: 0.8616 (t80) cc_final: 0.8062 (t80) REVERT: C 125 LYS cc_start: 0.8031 (tmtt) cc_final: 0.7571 (tptp) REVERT: C 127 MET cc_start: 0.8271 (mtt) cc_final: 0.7898 (mtm) REVERT: C 197 TRP cc_start: 0.4766 (t-100) cc_final: 0.4472 (t-100) REVERT: C 227 MET cc_start: 0.8449 (tmm) cc_final: 0.8085 (tpp) REVERT: D 77 TRP cc_start: 0.6607 (p-90) cc_final: 0.4731 (p-90) REVERT: D 123 THR cc_start: 0.8428 (p) cc_final: 0.8159 (p) REVERT: D 220 TYR cc_start: 0.8676 (t80) cc_final: 0.8052 (t80) REVERT: D 227 MET cc_start: 0.8512 (tmm) cc_final: 0.8231 (tpp) REVERT: D 440 TYR cc_start: 0.7549 (t80) cc_final: 0.7272 (t80) REVERT: E 197 TRP cc_start: 0.4909 (t-100) cc_final: 0.4590 (t-100) REVERT: E 222 GLN cc_start: 0.8304 (pm20) cc_final: 0.7935 (mp10) REVERT: E 239 MET cc_start: 0.8163 (ttt) cc_final: 0.7886 (ttt) REVERT: E 291 MET cc_start: 0.8984 (mmm) cc_final: 0.8779 (mmm) REVERT: E 440 TYR cc_start: 0.7501 (t80) cc_final: 0.7147 (t80) outliers start: 21 outliers final: 19 residues processed: 309 average time/residue: 0.0781 time to fit residues: 37.6740 Evaluate side-chains 295 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL 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: 7.9990 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 0.0070 chunk 88 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103406 restraints weight = 22740.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106960 restraints weight = 13230.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109474 restraints weight = 9336.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111120 restraints weight = 7380.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112327 restraints weight = 6302.951| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12881 Z= 0.181 Angle : 0.684 13.255 17688 Z= 0.333 Chirality : 0.046 0.196 2174 Planarity : 0.003 0.031 2123 Dihedral : 4.287 15.152 1876 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.17 % Allowed : 19.71 % Favored : 77.12 % 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 aren not related in a simple way. whole: -0.81 (0.20), residues: 1610 helix: 1.23 (0.21), residues: 535 sheet: -0.15 (0.31), residues: 335 loop : -2.15 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.019 0.002 TYR D 223 PHE 0.028 0.002 PHE A 425 TRP 0.017 0.001 TRP A 77 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00428 (12871) covalent geometry : angle 0.68362 (17663) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.63810 ( 10) hydrogen bonds : bond 0.04163 ( 586) hydrogen bonds : angle 4.80571 ( 1677) link_NAG-ASN : bond 0.00261 ( 5) link_NAG-ASN : angle 0.61812 ( 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 340 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.471 Fit side-chains REVERT: A 69 GLU cc_start: 0.8174 (tt0) cc_final: 0.7866 (tt0) REVERT: A 173 GLN cc_start: 0.8137 (pm20) cc_final: 0.7788 (pm20) REVERT: A 227 MET cc_start: 0.8440 (tmm) cc_final: 0.8056 (tpp) REVERT: A 431 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 23 HIS cc_start: 0.8684 (t-170) cc_final: 0.8456 (t-170) REVERT: B 129 VAL cc_start: 0.9174 (t) cc_final: 0.8954 (m) REVERT: B 270 ARG cc_start: 0.7423 (mmt-90) cc_final: 0.7103 (mpt-90) REVERT: B 287 TYR cc_start: 0.8687 (t80) cc_final: 0.8219 (t80) REVERT: C 125 LYS cc_start: 0.8104 (tmtt) cc_final: 0.7635 (tptp) REVERT: C 127 MET cc_start: 0.8257 (mtt) cc_final: 0.7902 (mtm) REVERT: C 197 TRP cc_start: 0.4841 (t-100) cc_final: 0.4538 (t-100) REVERT: C 222 GLN cc_start: 0.8161 (pm20) cc_final: 0.7776 (pm20) REVERT: C 223 TYR cc_start: 0.8851 (t80) cc_final: 0.8592 (t80) REVERT: C 227 MET cc_start: 0.8527 (tmm) cc_final: 0.8207 (tpp) REVERT: D 77 TRP cc_start: 0.6657 (p-90) cc_final: 0.4704 (p-90) REVERT: D 186 GLN cc_start: 0.8155 (pt0) cc_final: 0.7946 (tp40) REVERT: D 215 LYS cc_start: 0.8622 (tptp) cc_final: 0.7828 (pttm) REVERT: D 220 TYR cc_start: 0.8659 (t80) cc_final: 0.7966 (t80) REVERT: D 227 MET cc_start: 0.8508 (tmm) cc_final: 0.8250 (tpp) REVERT: D 440 TYR cc_start: 0.7591 (t80) cc_final: 0.7296 (t80) REVERT: E 197 TRP cc_start: 0.4908 (t-100) cc_final: 0.4549 (t-100) REVERT: E 222 GLN cc_start: 0.8358 (pm20) cc_final: 0.8152 (mp10) REVERT: E 239 MET cc_start: 0.8202 (ttt) cc_final: 0.7929 (ttt) REVERT: E 291 MET cc_start: 0.9003 (mmm) cc_final: 0.8472 (tpp) REVERT: E 440 TYR cc_start: 0.7510 (t80) cc_final: 0.7140 (t80) outliers start: 40 outliers final: 29 residues processed: 323 average time/residue: 0.0726 time to fit residues: 36.9096 Evaluate side-chains 301 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 271 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL 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 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 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: 0.9990 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 0.0170 chunk 133 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105249 restraints weight = 22513.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108912 restraints weight = 13119.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111483 restraints weight = 9254.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113264 restraints weight = 7304.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114521 restraints weight = 6202.186| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12881 Z= 0.133 Angle : 0.680 16.315 17688 Z= 0.325 Chirality : 0.045 0.258 2174 Planarity : 0.003 0.026 2123 Dihedral : 4.119 16.712 1876 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.61 % Allowed : 22.33 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.20), residues: 1610 helix: 1.31 (0.21), residues: 535 sheet: -0.04 (0.31), residues: 335 loop : -2.08 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 270 TYR 0.026 0.001 TYR D 223 PHE 0.019 0.002 PHE B 425 TRP 0.020 0.001 TRP A 77 HIS 0.002 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00307 (12871) covalent geometry : angle 0.68022 (17663) SS BOND : bond 0.00172 ( 5) SS BOND : angle 0.54610 ( 10) hydrogen bonds : bond 0.04014 ( 586) hydrogen bonds : angle 4.67577 ( 1677) link_NAG-ASN : bond 0.00357 ( 5) link_NAG-ASN : angle 0.34761 ( 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 344 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8428 (tmtt) REVERT: A 173 GLN cc_start: 0.8070 (pm20) cc_final: 0.7737 (pm20) REVERT: A 227 MET cc_start: 0.8453 (tmm) cc_final: 0.8038 (tpp) REVERT: B 23 HIS cc_start: 0.8662 (t-170) cc_final: 0.8430 (t-170) REVERT: B 129 VAL cc_start: 0.9156 (t) cc_final: 0.8929 (m) REVERT: B 231 LEU cc_start: 0.9193 (tt) cc_final: 0.8967 (tt) REVERT: B 287 TYR cc_start: 0.8677 (t80) cc_final: 0.8283 (t80) REVERT: C 125 LYS cc_start: 0.8069 (tmtt) cc_final: 0.7800 (tmtt) REVERT: C 173 GLN cc_start: 0.8115 (pm20) cc_final: 0.7809 (pm20) REVERT: C 197 TRP cc_start: 0.4762 (t-100) cc_final: 0.4479 (t-100) REVERT: C 222 GLN cc_start: 0.8189 (pm20) cc_final: 0.7826 (mp10) REVERT: C 223 TYR cc_start: 0.8838 (t80) cc_final: 0.8519 (t80) REVERT: C 227 MET cc_start: 0.8534 (tmm) cc_final: 0.8201 (tpp) REVERT: D 77 TRP cc_start: 0.6638 (p-90) cc_final: 0.4655 (p-90) REVERT: D 186 GLN cc_start: 0.8201 (pt0) cc_final: 0.7969 (tp40) REVERT: D 215 LYS cc_start: 0.8594 (tptp) cc_final: 0.7806 (pttm) REVERT: D 220 TYR cc_start: 0.8645 (t80) cc_final: 0.8024 (t80) REVERT: D 227 MET cc_start: 0.8500 (tmm) cc_final: 0.8091 (tpp) REVERT: D 440 TYR cc_start: 0.7599 (t80) cc_final: 0.7332 (t80) REVERT: E 81 ASP cc_start: 0.7062 (p0) cc_final: 0.6466 (t70) REVERT: E 117 LEU cc_start: 0.8601 (tp) cc_final: 0.8309 (tp) REVERT: E 125 LYS cc_start: 0.8465 (tttp) cc_final: 0.7871 (tptp) REVERT: E 197 TRP cc_start: 0.4834 (t-100) cc_final: 0.4486 (t-100) REVERT: E 222 GLN cc_start: 0.8383 (pm20) cc_final: 0.8140 (mp10) REVERT: E 239 MET cc_start: 0.8201 (ttt) cc_final: 0.7948 (ttt) REVERT: E 289 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8274 (t80) REVERT: E 291 MET cc_start: 0.8993 (mmm) cc_final: 0.8591 (mmm) REVERT: E 440 TYR cc_start: 0.7490 (t80) cc_final: 0.7110 (t80) outliers start: 33 outliers final: 25 residues processed: 327 average time/residue: 0.0749 time to fit residues: 38.0846 Evaluate side-chains 306 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 289 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 119 optimal weight: 0.4980 chunk 79 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 90 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN E 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104573 restraints weight = 22402.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108179 restraints weight = 13180.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110697 restraints weight = 9360.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112459 restraints weight = 7425.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113587 restraints weight = 6323.893| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2319 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= 0.140 Angle : 0.680 15.694 17688 Z= 0.326 Chirality : 0.045 0.230 2174 Planarity : 0.003 0.027 2123 Dihedral : 4.043 16.451 1876 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.77 % Allowed : 23.12 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.20), residues: 1610 helix: 1.27 (0.21), residues: 535 sheet: 0.12 (0.31), residues: 330 loop : -2.09 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.023 0.001 TYR E 287 PHE 0.027 0.002 PHE A 425 TRP 0.022 0.001 TRP A 77 HIS 0.004 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00327 (12871) covalent geometry : angle 0.68044 (17663) SS BOND : bond 0.00176 ( 5) SS BOND : angle 0.52067 ( 10) hydrogen bonds : bond 0.04027 ( 586) hydrogen bonds : angle 4.68538 ( 1677) link_NAG-ASN : bond 0.00309 ( 5) link_NAG-ASN : angle 0.43015 ( 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 333 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8236 (tt0) cc_final: 0.8035 (tt0) REVERT: A 125 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8487 (tmtt) REVERT: A 173 GLN cc_start: 0.8070 (pm20) cc_final: 0.7736 (pm20) REVERT: A 227 MET cc_start: 0.8455 (tmm) cc_final: 0.8061 (tpp) REVERT: B 23 HIS cc_start: 0.8685 (t-170) cc_final: 0.8464 (t-170) REVERT: B 129 VAL cc_start: 0.9148 (t) cc_final: 0.8922 (m) REVERT: B 270 ARG cc_start: 0.7360 (mmt-90) cc_final: 0.7079 (mpt-90) REVERT: B 287 TYR cc_start: 0.8637 (t80) cc_final: 0.8295 (t80) REVERT: C 125 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7566 (tptp) REVERT: C 173 GLN cc_start: 0.8123 (pm20) cc_final: 0.7822 (pm20) REVERT: C 197 TRP cc_start: 0.4845 (t-100) cc_final: 0.4560 (t-100) REVERT: C 222 GLN cc_start: 0.8172 (pm20) cc_final: 0.7908 (mp10) REVERT: C 227 MET cc_start: 0.8546 (tmm) cc_final: 0.8100 (tpp) REVERT: C 239 MET cc_start: 0.8179 (ttt) cc_final: 0.7881 (ttt) REVERT: D 77 TRP cc_start: 0.6638 (p-90) cc_final: 0.4624 (p-90) REVERT: D 186 GLN cc_start: 0.8204 (pt0) cc_final: 0.7977 (tp40) REVERT: D 215 LYS cc_start: 0.8595 (tptp) cc_final: 0.7799 (pttm) REVERT: D 220 TYR cc_start: 0.8622 (t80) cc_final: 0.7975 (t80) REVERT: D 227 MET cc_start: 0.8500 (tmm) cc_final: 0.8119 (tpp) REVERT: D 440 TYR cc_start: 0.7590 (t80) cc_final: 0.7293 (t80) REVERT: E 197 TRP cc_start: 0.4824 (t-100) cc_final: 0.4470 (t-100) REVERT: E 220 TYR cc_start: 0.8792 (t80) cc_final: 0.8482 (t80) REVERT: E 222 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: E 239 MET cc_start: 0.8200 (ttt) cc_final: 0.7889 (ttt) REVERT: E 241 PHE cc_start: 0.7981 (m-80) cc_final: 0.7575 (m-80) REVERT: E 289 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8460 (t80) REVERT: E 291 MET cc_start: 0.9043 (mmm) cc_final: 0.8645 (mmm) REVERT: E 301 MET cc_start: 0.7856 (mmt) cc_final: 0.7249 (mmm) REVERT: E 440 TYR cc_start: 0.7505 (t80) cc_final: 0.7150 (t80) outliers start: 35 outliers final: 30 residues processed: 317 average time/residue: 0.0737 time to fit residues: 36.5699 Evaluate side-chains 315 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 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 C residue 45 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain 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 119 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 50 VAL 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 222 GLN 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: 0.8980 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103526 restraints weight = 22602.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107096 restraints weight = 13257.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109593 restraints weight = 9426.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111263 restraints weight = 7495.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112529 restraints weight = 6421.214| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2395 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= 0.144 Angle : 0.689 15.030 17688 Z= 0.330 Chirality : 0.045 0.227 2174 Planarity : 0.003 0.027 2123 Dihedral : 4.014 15.976 1876 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.72 % Allowed : 23.91 % Favored : 72.37 % 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 aren not related in a simple way. whole: -0.64 (0.20), residues: 1610 helix: 1.34 (0.21), residues: 530 sheet: 0.17 (0.31), residues: 330 loop : -2.10 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 270 TYR 0.023 0.001 TYR E 287 PHE 0.024 0.002 PHE E 425 TRP 0.026 0.001 TRP A 77 HIS 0.002 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00339 (12871) covalent geometry : angle 0.68963 (17663) SS BOND : bond 0.00178 ( 5) SS BOND : angle 0.52480 ( 10) hydrogen bonds : bond 0.03980 ( 586) hydrogen bonds : angle 4.69155 ( 1677) link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 0.47462 ( 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 339 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8475 (tmm) cc_final: 0.8074 (tpp) REVERT: B 23 HIS cc_start: 0.8659 (t-170) cc_final: 0.8424 (t-170) REVERT: B 129 VAL cc_start: 0.9126 (t) cc_final: 0.8914 (m) REVERT: B 227 MET cc_start: 0.8490 (tmm) cc_final: 0.7999 (tmm) REVERT: C 125 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7768 (tptp) REVERT: C 173 GLN cc_start: 0.8121 (pm20) cc_final: 0.7810 (pm20) REVERT: C 197 TRP cc_start: 0.4864 (t-100) cc_final: 0.4569 (t-100) REVERT: C 222 GLN cc_start: 0.8138 (pm20) cc_final: 0.7921 (mp10) REVERT: C 227 MET cc_start: 0.8553 (tmm) cc_final: 0.8161 (tpp) REVERT: D 77 TRP cc_start: 0.6568 (p-90) cc_final: 0.4546 (p-90) REVERT: D 186 GLN cc_start: 0.8233 (pt0) cc_final: 0.8016 (tp40) REVERT: D 215 LYS cc_start: 0.8597 (tptp) cc_final: 0.7838 (pttm) REVERT: D 220 TYR cc_start: 0.8624 (t80) cc_final: 0.7969 (t80) REVERT: D 227 MET cc_start: 0.8504 (tmm) cc_final: 0.8144 (tpp) REVERT: D 440 TYR cc_start: 0.7604 (t80) cc_final: 0.7295 (t80) REVERT: E 197 TRP cc_start: 0.4857 (t-100) cc_final: 0.4505 (t-100) REVERT: E 220 TYR cc_start: 0.8738 (t80) cc_final: 0.8466 (t80) REVERT: E 222 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8189 (mp10) REVERT: E 239 MET cc_start: 0.8164 (ttt) cc_final: 0.7869 (ttt) REVERT: E 289 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8457 (t80) REVERT: E 291 MET cc_start: 0.9049 (mmm) cc_final: 0.8633 (mmm) REVERT: E 301 MET cc_start: 0.7844 (mmt) cc_final: 0.7239 (mmm) REVERT: E 440 TYR cc_start: 0.7502 (t80) cc_final: 0.7137 (t80) outliers start: 47 outliers final: 36 residues processed: 322 average time/residue: 0.0760 time to fit residues: 38.7031 Evaluate side-chains 317 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ASP 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 155 VAL Chi-restraints excluded: chain C residue 224 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 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 224 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: 0.6980 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102014 restraints weight = 22558.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105540 restraints weight = 13311.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108031 restraints weight = 9447.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109707 restraints weight = 7502.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110916 restraints weight = 6422.459| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12881 Z= 0.161 Angle : 0.709 14.605 17688 Z= 0.340 Chirality : 0.045 0.232 2174 Planarity : 0.003 0.028 2123 Dihedral : 4.024 16.362 1876 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.56 % Allowed : 24.62 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.21), residues: 1610 helix: 1.36 (0.21), residues: 535 sheet: 0.18 (0.31), residues: 330 loop : -2.09 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 270 TYR 0.025 0.002 TYR E 287 PHE 0.039 0.002 PHE B 425 TRP 0.030 0.001 TRP A 77 HIS 0.004 0.000 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00381 (12871) covalent geometry : angle 0.70943 (17663) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.53349 ( 10) hydrogen bonds : bond 0.04046 ( 586) hydrogen bonds : angle 4.71698 ( 1677) link_NAG-ASN : bond 0.00214 ( 5) link_NAG-ASN : angle 0.58401 ( 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: 45 poor density : 298 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8611 (tttm) cc_final: 0.8359 (tptp) REVERT: A 227 MET cc_start: 0.8484 (tmm) cc_final: 0.7890 (tpp) REVERT: A 231 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8985 (tp) REVERT: B 23 HIS cc_start: 0.8673 (t-170) cc_final: 0.8455 (t-170) REVERT: B 87 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8298 (mmmm) REVERT: B 129 VAL cc_start: 0.9140 (t) cc_final: 0.8937 (m) REVERT: B 227 MET cc_start: 0.8527 (tmm) cc_final: 0.8048 (tmm) REVERT: B 287 TYR cc_start: 0.8697 (t80) cc_final: 0.8412 (t80) REVERT: C 125 LYS cc_start: 0.8203 (tmtt) cc_final: 0.7736 (tptp) REVERT: C 173 GLN cc_start: 0.8113 (pm20) cc_final: 0.7824 (pm20) REVERT: C 197 TRP cc_start: 0.4944 (t-100) cc_final: 0.4647 (t-100) REVERT: C 227 MET cc_start: 0.8591 (tmm) cc_final: 0.8237 (tpp) REVERT: D 77 TRP cc_start: 0.6618 (p-90) cc_final: 0.5223 (p-90) REVERT: D 127 MET cc_start: 0.8370 (mtt) cc_final: 0.8144 (mtm) REVERT: D 186 GLN cc_start: 0.8269 (pt0) cc_final: 0.8060 (tp40) REVERT: D 215 LYS cc_start: 0.8603 (tptp) cc_final: 0.7869 (pttm) REVERT: D 220 TYR cc_start: 0.8631 (t80) cc_final: 0.8020 (t80) REVERT: D 227 MET cc_start: 0.8514 (tmm) cc_final: 0.8143 (tpp) REVERT: D 440 TYR cc_start: 0.7625 (t80) cc_final: 0.7338 (t80) REVERT: E 197 TRP cc_start: 0.4929 (t-100) cc_final: 0.4563 (t-100) REVERT: E 220 TYR cc_start: 0.8753 (t80) cc_final: 0.8481 (t80) REVERT: E 222 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: E 239 MET cc_start: 0.8157 (ttt) cc_final: 0.7881 (ttt) REVERT: E 289 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8471 (t80) REVERT: E 291 MET cc_start: 0.9053 (mmm) cc_final: 0.8650 (mmm) REVERT: E 440 TYR cc_start: 0.7420 (t80) cc_final: 0.7096 (t80) outliers start: 45 outliers final: 35 residues processed: 328 average time/residue: 0.0776 time to fit residues: 39.5904 Evaluate side-chains 319 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 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 155 VAL Chi-restraints excluded: chain C residue 224 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 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 122 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 222 GLN Chi-restraints excluded: chain E residue 224 VAL 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: 4.9990 chunk 127 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104944 restraints weight = 22502.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108483 restraints weight = 13464.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110967 restraints weight = 9633.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112663 restraints weight = 7671.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113735 restraints weight = 6564.168| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2654 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= 0.131 Angle : 0.718 15.625 17688 Z= 0.343 Chirality : 0.046 0.224 2174 Planarity : 0.003 0.027 2123 Dihedral : 4.034 16.347 1876 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.17 % Allowed : 25.26 % Favored : 71.58 % 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 aren not related in a simple way. whole: -0.61 (0.20), residues: 1610 helix: 1.34 (0.21), residues: 530 sheet: 0.13 (0.31), residues: 335 loop : -2.04 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 270 TYR 0.024 0.001 TYR E 287 PHE 0.026 0.002 PHE B 425 TRP 0.033 0.001 TRP A 77 HIS 0.003 0.000 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00301 (12871) covalent geometry : angle 0.71876 (17663) SS BOND : bond 0.00149 ( 5) SS BOND : angle 0.46133 ( 10) hydrogen bonds : bond 0.04017 ( 586) hydrogen bonds : angle 4.72046 ( 1677) link_NAG-ASN : bond 0.00345 ( 5) link_NAG-ASN : angle 0.38224 ( 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 339 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8556 (tttm) cc_final: 0.8241 (tptp) REVERT: A 155 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8226 (p) REVERT: A 173 GLN cc_start: 0.7978 (pm20) cc_final: 0.7679 (pm20) REVERT: A 227 MET cc_start: 0.8460 (tmm) cc_final: 0.7964 (tpp) REVERT: A 231 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8926 (tp) REVERT: A 239 MET cc_start: 0.8079 (ttt) cc_final: 0.7825 (ttt) REVERT: B 23 HIS cc_start: 0.8627 (t-170) cc_final: 0.8414 (t-170) REVERT: B 129 VAL cc_start: 0.9137 (t) cc_final: 0.8927 (m) REVERT: B 287 TYR cc_start: 0.8597 (t80) cc_final: 0.8319 (t80) REVERT: B 291 MET cc_start: 0.8539 (tpp) cc_final: 0.8171 (tpp) REVERT: B 440 TYR cc_start: 0.7341 (t80) cc_final: 0.6970 (t80) REVERT: C 125 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7722 (tptp) REVERT: C 173 GLN cc_start: 0.8176 (pm20) cc_final: 0.7898 (pm20) REVERT: C 197 TRP cc_start: 0.4821 (t-100) cc_final: 0.4515 (t-100) REVERT: C 227 MET cc_start: 0.8605 (tmm) cc_final: 0.8279 (tpp) REVERT: D 77 TRP cc_start: 0.6581 (p-90) cc_final: 0.5208 (p-90) REVERT: D 215 LYS cc_start: 0.8592 (tptp) cc_final: 0.7898 (pttm) REVERT: D 220 TYR cc_start: 0.8627 (t80) cc_final: 0.8091 (t80) REVERT: D 440 TYR cc_start: 0.7652 (t80) cc_final: 0.7338 (t80) REVERT: E 117 LEU cc_start: 0.8623 (tp) cc_final: 0.8376 (tp) REVERT: E 197 TRP cc_start: 0.4808 (t-100) cc_final: 0.4443 (t-100) REVERT: E 220 TYR cc_start: 0.8748 (t80) cc_final: 0.8468 (t80) REVERT: E 239 MET cc_start: 0.8074 (ttt) cc_final: 0.7804 (ttt) REVERT: E 289 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8416 (t80) REVERT: E 291 MET cc_start: 0.9057 (mmm) cc_final: 0.8691 (mmm) REVERT: E 440 TYR cc_start: 0.7379 (t80) cc_final: 0.7073 (t80) outliers start: 40 outliers final: 29 residues processed: 324 average time/residue: 0.0780 time to fit residues: 39.4892 Evaluate side-chains 313 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 281 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 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 155 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 256 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 50 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 155 VAL 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: 0.9980 chunk 59 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 123 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** 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 = 0.3627 r_free = 0.3627 target = 0.131639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105076 restraints weight = 22492.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108552 restraints weight = 13526.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111038 restraints weight = 9714.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112631 restraints weight = 7746.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113872 restraints weight = 6669.868| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12881 Z= 0.137 Angle : 0.740 15.752 17688 Z= 0.352 Chirality : 0.047 0.376 2174 Planarity : 0.003 0.036 2123 Dihedral : 4.028 16.480 1876 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.69 % Allowed : 27.32 % Favored : 69.99 % 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 aren not related in a simple way. whole: -0.58 (0.21), residues: 1610 helix: 1.31 (0.21), residues: 535 sheet: 0.29 (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 0.030 0.002 TYR E 287 PHE 0.040 0.002 PHE A 234 TRP 0.036 0.001 TRP A 77 HIS 0.003 0.000 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00317 (12871) covalent geometry : angle 0.74070 (17663) SS BOND : bond 0.00151 ( 5) SS BOND : angle 0.45687 ( 10) hydrogen bonds : bond 0.04055 ( 586) hydrogen bonds : angle 4.76790 ( 1677) link_NAG-ASN : bond 0.00330 ( 5) link_NAG-ASN : angle 0.55402 ( 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 320 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8556 (tttm) cc_final: 0.8235 (tptp) REVERT: A 173 GLN cc_start: 0.8011 (pm20) cc_final: 0.7701 (pm20) REVERT: A 186 GLN cc_start: 0.8240 (tt0) cc_final: 0.7537 (tp40) REVERT: A 227 MET cc_start: 0.8437 (tmm) cc_final: 0.8049 (tpp) REVERT: A 231 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8917 (tp) REVERT: A 239 MET cc_start: 0.8075 (ttt) cc_final: 0.7836 (ttt) REVERT: B 239 MET cc_start: 0.7766 (tmm) cc_final: 0.7504 (ttm) REVERT: B 287 TYR cc_start: 0.8591 (t80) cc_final: 0.8355 (t80) REVERT: B 440 TYR cc_start: 0.7328 (t80) cc_final: 0.6961 (t80) REVERT: C 125 LYS cc_start: 0.8107 (tmtt) cc_final: 0.7558 (tptp) REVERT: C 173 GLN cc_start: 0.8230 (pm20) cc_final: 0.7981 (pm20) REVERT: C 197 TRP cc_start: 0.4796 (t-100) cc_final: 0.4466 (t-100) REVERT: C 227 MET cc_start: 0.8646 (tmm) cc_final: 0.8338 (tpp) REVERT: D 77 TRP cc_start: 0.6646 (p-90) cc_final: 0.5247 (p-90) REVERT: D 215 LYS cc_start: 0.8562 (tptp) cc_final: 0.7964 (pttt) REVERT: D 220 TYR cc_start: 0.8615 (t80) cc_final: 0.8068 (t80) REVERT: D 291 MET cc_start: 0.8400 (tpp) cc_final: 0.7790 (tpp) REVERT: D 440 TYR cc_start: 0.7665 (t80) cc_final: 0.7344 (t80) REVERT: E 197 TRP cc_start: 0.4772 (t-100) cc_final: 0.4403 (t-100) REVERT: E 227 MET cc_start: 0.8627 (tmm) cc_final: 0.8197 (tpp) REVERT: E 239 MET cc_start: 0.8037 (ttt) cc_final: 0.7768 (ttt) REVERT: E 289 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8427 (t80) REVERT: E 440 TYR cc_start: 0.7347 (t80) cc_final: 0.7054 (t80) outliers start: 34 outliers final: 30 residues processed: 309 average time/residue: 0.0769 time to fit residues: 36.9898 Evaluate side-chains 309 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 277 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 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 155 VAL Chi-restraints excluded: chain C residue 224 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 256 LEU Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 289 PHE 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: 7.9990 chunk 108 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 304 ASN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.125515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.099504 restraints weight = 22926.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102680 restraints weight = 14324.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104897 restraints weight = 10503.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106422 restraints weight = 8516.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107454 restraints weight = 7380.150| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12881 Z= 0.232 Angle : 0.780 15.586 17688 Z= 0.381 Chirality : 0.049 0.349 2174 Planarity : 0.004 0.038 2123 Dihedral : 4.275 18.086 1876 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.01 % Allowed : 27.32 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.21), residues: 1610 helix: 1.27 (0.21), residues: 530 sheet: 0.12 (0.32), residues: 330 loop : -2.16 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 270 TYR 0.023 0.002 TYR E 287 PHE 0.037 0.003 PHE E 425 TRP 0.022 0.002 TRP A 77 HIS 0.005 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00553 (12871) covalent geometry : angle 0.77980 (17663) SS BOND : bond 0.00248 ( 5) SS BOND : angle 0.64470 ( 10) hydrogen bonds : bond 0.04360 ( 586) hydrogen bonds : angle 4.93645 ( 1677) link_NAG-ASN : bond 0.00022 ( 5) link_NAG-ASN : angle 0.98854 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.33 seconds wall clock time: 34 minutes 32.94 seconds (2072.94 seconds total)