Starting phenix.real_space_refine on Sat Aug 23 16:18:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wge_37511/08_2025/8wge_37511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wge_37511/08_2025/8wge_37511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wge_37511/08_2025/8wge_37511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wge_37511/08_2025/8wge_37511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wge_37511/08_2025/8wge_37511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wge_37511/08_2025/8wge_37511.map" } resolution = 3.4 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= 0.000 sd= 0.005 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 110 5.16 5 C 8765 2.51 5 N 2210 2.21 5 O 2430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 13515 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2689 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.04, per 1000 atoms: 0.22 Number of scatterers: 13515 At special positions: 0 Unit cell: (86.1, 83.64, 155.8, 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 110 16.00 O 2430 8.00 N 2210 7.00 C 8765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 147 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 161 " 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 132 " " NAG B 501 " - " ASN B 132 " " NAG C 501 " - " ASN C 132 " " NAG D 501 " - " ASN D 132 " " NAG E 501 " - " ASN E 132 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 507.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 22 sheets defined 42.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 4.054A pdb=" N GLU A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 217 through 238 removed outlier: 5.015A pdb=" N LEU A 226 " --> pdb=" O MET A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 279 through 308 Processing helix chain 'A' and resid 351 through 406 removed outlier: 3.601A pdb=" N VAL A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 removed outlier: 4.032A pdb=" N GLU B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 217 through 224 removed outlier: 3.631A pdb=" N MET B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 238 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 248 through 268 removed outlier: 3.608A pdb=" N LEU B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 308 Processing helix chain 'B' and resid 351 through 405 removed outlier: 3.654A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.942A pdb=" N GLU C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.599A pdb=" N MET C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 248 through 268 removed outlier: 3.607A pdb=" N LEU C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 308 Processing helix chain 'C' and resid 351 through 405 removed outlier: 3.610A pdb=" N VAL C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C 378 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.989A pdb=" N GLU D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 217 through 224 removed outlier: 3.642A pdb=" N MET D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 239 through 241 No H-bonds generated for 'chain 'D' and resid 239 through 241' Processing helix chain 'D' and resid 248 through 268 removed outlier: 3.607A pdb=" N LEU D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 308 Processing helix chain 'D' and resid 351 through 405 removed outlier: 3.636A pdb=" N VAL D 356 " --> pdb=" O MET D 352 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.982A pdb=" N GLU E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 217 through 224 removed outlier: 3.562A pdb=" N MET E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 238 Processing helix chain 'E' and resid 239 through 241 No H-bonds generated for 'chain 'E' and resid 239 through 241' Processing helix chain 'E' and resid 248 through 268 removed outlier: 3.604A pdb=" N LEU E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.504A pdb=" N ARG E 303 " --> pdb=" O MET E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 405 removed outlier: 3.685A pdb=" N VAL E 356 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL E 357 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.009A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 144 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N SER A 117 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 101 removed outlier: 8.009A pdb=" N ASP A 126 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU A 138 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 70 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 64 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 164 removed outlier: 7.241A pdb=" N PHE A 208 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU A 199 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA A 210 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A 197 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY A 212 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 144 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N SER B 117 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP B 126 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B 138 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 70 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 64 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 72 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 164 removed outlier: 7.230A pdb=" N PHE B 208 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU B 199 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 210 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 197 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 212 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 144 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER C 117 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 97 through 101 removed outlier: 7.998A pdb=" N ASP C 126 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU C 138 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C 134 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG C 70 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL C 64 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN C 72 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 158 through 164 removed outlier: 7.285A pdb=" N PHE C 208 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU C 199 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 210 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA C 197 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY C 212 " --> pdb=" O THR C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 101 removed outlier: 7.990A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 144 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER D 117 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 101 removed outlier: 7.990A pdb=" N ASP D 126 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU D 138 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR D 134 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG D 70 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL D 64 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN D 72 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AB8, first strand: chain 'D' and resid 158 through 164 removed outlier: 7.243A pdb=" N PHE D 208 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LEU D 199 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA D 210 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA D 197 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY D 212 " --> pdb=" O THR D 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.002A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU E 144 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER E 117 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 97 through 101 removed outlier: 8.002A pdb=" N ASP E 126 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU E 138 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG E 70 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL E 64 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN E 72 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AC4, first strand: chain 'E' and resid 158 through 164 removed outlier: 7.207A pdb=" N PHE E 208 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LEU E 199 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA E 210 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA E 197 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY E 212 " --> pdb=" O THR E 195 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4280 1.34 - 1.46: 2916 1.46 - 1.58: 6419 1.58 - 1.69: 0 1.69 - 1.81: 175 Bond restraints: 13790 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 13785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 18184 1.04 - 2.07: 462 2.07 - 3.11: 109 3.11 - 4.15: 17 4.15 - 5.18: 18 Bond angle restraints: 18790 Sorted by residual: angle pdb=" N PRO E 155 " pdb=" CA PRO E 155 " pdb=" C PRO E 155 " ideal model delta sigma weight residual 112.10 116.50 -4.40 2.60e+00 1.48e-01 2.87e+00 angle pdb=" N VAL D 112 " pdb=" CA VAL D 112 " pdb=" C VAL D 112 " ideal model delta sigma weight residual 109.34 105.85 3.49 2.08e+00 2.31e-01 2.82e+00 angle pdb=" CA PHE A 56 " pdb=" CB PHE A 56 " pdb=" CG PHE A 56 " ideal model delta sigma weight residual 113.80 115.47 -1.67 1.00e+00 1.00e+00 2.78e+00 angle pdb=" N VAL D 404 " pdb=" CA VAL D 404 " pdb=" C VAL D 404 " ideal model delta sigma weight residual 109.34 112.78 -3.44 2.08e+00 2.31e-01 2.74e+00 angle pdb=" N PRO B 155 " pdb=" CA PRO B 155 " pdb=" C PRO B 155 " ideal model delta sigma weight residual 112.10 116.40 -4.30 2.60e+00 1.48e-01 2.73e+00 ... (remaining 18785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 7311 17.72 - 35.43: 771 35.43 - 53.15: 219 53.15 - 70.86: 19 70.86 - 88.58: 20 Dihedral angle restraints: 8340 sinusoidal: 3235 harmonic: 5105 Sorted by residual: dihedral pdb=" CB CYS B 147 " pdb=" SG CYS B 147 " pdb=" SG CYS B 161 " pdb=" CB CYS B 161 " ideal model delta sinusoidal sigma weight residual 93.00 166.46 -73.46 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS C 147 " pdb=" SG CYS C 147 " pdb=" SG CYS C 161 " pdb=" CB CYS C 161 " ideal model delta sinusoidal sigma weight residual 93.00 166.41 -73.41 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 161 " pdb=" CB CYS E 161 " ideal model delta sinusoidal sigma weight residual 93.00 166.36 -73.36 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 8337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1389 0.026 - 0.051: 551 0.051 - 0.077: 184 0.077 - 0.102: 85 0.102 - 0.128: 81 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CA ILE B 165 " pdb=" N ILE B 165 " pdb=" C ILE B 165 " pdb=" CB ILE B 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE D 165 " pdb=" N ILE D 165 " pdb=" C ILE D 165 " pdb=" CB ILE D 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2287 not shown) Planarity restraints: 2350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 56 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C PHE A 56 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 56 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 57 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 56 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C PHE C 56 " 0.025 2.00e-02 2.50e+03 pdb=" O PHE C 56 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE C 57 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 154 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 155 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " -0.018 5.00e-02 4.00e+02 ... (remaining 2347 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3711 2.81 - 3.34: 12223 3.34 - 3.86: 22050 3.86 - 4.38: 25148 4.38 - 4.90: 45145 Nonbonded interactions: 108277 Sorted by model distance: nonbonded pdb=" NH2 ARG B 70 " pdb=" O LEU C 62 " model vdw 2.292 3.120 nonbonded pdb=" O THR A 175 " pdb=" OG1 THR A 175 " model vdw 2.300 3.040 nonbonded pdb=" O THR B 175 " pdb=" OG1 THR B 175 " model vdw 2.301 3.040 nonbonded pdb=" NH2 ARG D 70 " pdb=" O LEU E 62 " model vdw 2.303 3.120 nonbonded pdb=" O THR D 175 " pdb=" OG1 THR D 175 " model vdw 2.304 3.040 ... (remaining 108272 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.860 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.002 0.026 13805 Z= 0.097 Angle : 0.444 5.183 18825 Z= 0.218 Chirality : 0.039 0.128 2290 Planarity : 0.003 0.036 2345 Dihedral : 15.644 88.577 4990 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.34 % Allowed : 15.81 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.72 (0.21), residues: 1720 helix: 1.68 (0.19), residues: 695 sheet: 0.17 (0.25), residues: 495 loop : -0.73 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.012 0.001 TYR E 59 PHE 0.019 0.001 PHE E 385 TRP 0.003 0.000 TRP D 192 HIS 0.008 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00214 (13790) covalent geometry : angle 0.44413 (18790) SS BOND : bond 0.00112 ( 10) SS BOND : angle 0.52304 ( 20) hydrogen bonds : bond 0.21034 ( 761) hydrogen bonds : angle 6.72131 ( 2382) link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 0.59979 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 241 time to evaluate : 0.527 Fit side-chains REVERT: C 222 MET cc_start: 0.7598 (mtp) cc_final: 0.7312 (mtt) REVERT: D 56 PHE cc_start: 0.7568 (t80) cc_final: 0.7315 (t80) REVERT: D 222 MET cc_start: 0.7658 (mtp) cc_final: 0.7339 (mtt) outliers start: 5 outliers final: 1 residues processed: 241 average time/residue: 0.0967 time to fit residues: 35.2103 Evaluate side-chains 225 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 403 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS D 374 HIS E 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.123968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.100466 restraints weight = 15577.075| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.88 r_work: 0.2865 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13805 Z= 0.150 Angle : 0.526 6.872 18825 Z= 0.267 Chirality : 0.042 0.142 2290 Planarity : 0.004 0.032 2345 Dihedral : 4.013 24.627 1953 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.69 % Allowed : 15.61 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.00 (0.21), residues: 1720 helix: 2.39 (0.19), residues: 690 sheet: -0.11 (0.24), residues: 520 loop : -0.85 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 248 TYR 0.016 0.001 TYR D 406 PHE 0.014 0.002 PHE E 384 TRP 0.007 0.001 TRP D 81 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00355 (13790) covalent geometry : angle 0.52519 (18790) SS BOND : bond 0.00092 ( 10) SS BOND : angle 0.77872 ( 20) hydrogen bonds : bond 0.05248 ( 761) hydrogen bonds : angle 4.47977 ( 2382) link_NAG-ASN : bond 0.00077 ( 5) link_NAG-ASN : angle 0.83774 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.554 Fit side-chains REVERT: A 56 PHE cc_start: 0.7625 (t80) cc_final: 0.7355 (t80) REVERT: B 33 MET cc_start: 0.8045 (ttp) cc_final: 0.7625 (ttm) REVERT: B 259 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 403 MET cc_start: 0.7908 (ttp) cc_final: 0.7645 (ttp) REVERT: C 127 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8848 (pp) REVERT: C 222 MET cc_start: 0.7684 (mtp) cc_final: 0.7368 (mtt) REVERT: C 403 MET cc_start: 0.8047 (ttp) cc_final: 0.7829 (ttp) REVERT: D 56 PHE cc_start: 0.7631 (t80) cc_final: 0.7172 (t80) REVERT: E 259 PHE cc_start: 0.8282 (OUTLIER) cc_final: 0.7535 (t80) REVERT: E 379 LYS cc_start: 0.7792 (mptt) cc_final: 0.7183 (ttpt) outliers start: 25 outliers final: 15 residues processed: 244 average time/residue: 0.0977 time to fit residues: 36.9710 Evaluate side-chains 230 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN D 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.120936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.097196 restraints weight = 15735.465| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.89 r_work: 0.2821 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13805 Z= 0.211 Angle : 0.587 7.887 18825 Z= 0.291 Chirality : 0.043 0.143 2290 Planarity : 0.004 0.028 2345 Dihedral : 4.132 16.608 1950 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.11 % Allowed : 15.68 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.88 (0.21), residues: 1720 helix: 2.25 (0.19), residues: 690 sheet: -0.24 (0.24), residues: 510 loop : -0.77 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 248 TYR 0.015 0.002 TYR B 406 PHE 0.016 0.002 PHE A 251 TRP 0.005 0.001 TRP E 88 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00521 (13790) covalent geometry : angle 0.58575 (18790) SS BOND : bond 0.00060 ( 10) SS BOND : angle 0.92102 ( 20) hydrogen bonds : bond 0.05403 ( 761) hydrogen bonds : angle 4.46338 ( 2382) link_NAG-ASN : bond 0.00252 ( 5) link_NAG-ASN : angle 0.98937 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.550 Fit side-chains REVERT: A 56 PHE cc_start: 0.7615 (t80) cc_final: 0.7168 (t80) REVERT: B 33 MET cc_start: 0.8266 (ttp) cc_final: 0.7773 (ttm) REVERT: B 39 MET cc_start: 0.8583 (mmt) cc_final: 0.8368 (mmt) REVERT: B 379 LYS cc_start: 0.7908 (mptt) cc_final: 0.7307 (ttpt) REVERT: C 379 LYS cc_start: 0.7814 (mptt) cc_final: 0.7227 (ttpt) REVERT: D 42 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7551 (ptm) REVERT: D 56 PHE cc_start: 0.7718 (t80) cc_final: 0.7320 (t80) REVERT: E 259 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7603 (t80) REVERT: E 379 LYS cc_start: 0.7772 (mptt) cc_final: 0.7158 (ttpt) REVERT: E 393 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7984 (mm) outliers start: 46 outliers final: 27 residues processed: 239 average time/residue: 0.1118 time to fit residues: 40.3177 Evaluate side-chains 237 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.102665 restraints weight = 15490.738| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.70 r_work: 0.2890 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13805 Z= 0.126 Angle : 0.509 8.635 18825 Z= 0.251 Chirality : 0.040 0.132 2290 Planarity : 0.003 0.027 2345 Dihedral : 3.800 14.178 1950 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.50 % Allowed : 16.82 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.04 (0.21), residues: 1720 helix: 2.60 (0.19), residues: 685 sheet: -0.31 (0.24), residues: 520 loop : -0.81 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 248 TYR 0.012 0.001 TYR B 406 PHE 0.015 0.001 PHE C 384 TRP 0.006 0.001 TRP D 81 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00293 (13790) covalent geometry : angle 0.50908 (18790) SS BOND : bond 0.00079 ( 10) SS BOND : angle 0.61891 ( 20) hydrogen bonds : bond 0.04538 ( 761) hydrogen bonds : angle 4.16726 ( 2382) link_NAG-ASN : bond 0.00023 ( 5) link_NAG-ASN : angle 0.78090 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.537 Fit side-chains REVERT: A 56 PHE cc_start: 0.7307 (t80) cc_final: 0.6864 (t80) REVERT: B 33 MET cc_start: 0.8053 (ttp) cc_final: 0.7621 (ttm) REVERT: B 127 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8831 (pp) REVERT: B 259 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7658 (t80) REVERT: B 379 LYS cc_start: 0.7787 (mptt) cc_final: 0.7283 (ttpt) REVERT: C 127 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8937 (pp) REVERT: D 42 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7540 (ptm) REVERT: D 56 PHE cc_start: 0.7438 (t80) cc_final: 0.7082 (t80) REVERT: D 259 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7696 (t80) REVERT: D 379 LYS cc_start: 0.7782 (mptt) cc_final: 0.7258 (ttpt) REVERT: E 259 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7549 (t80) REVERT: E 379 LYS cc_start: 0.7793 (mptt) cc_final: 0.7258 (ttpt) REVERT: E 393 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7986 (mm) outliers start: 37 outliers final: 24 residues processed: 255 average time/residue: 0.1050 time to fit residues: 41.1390 Evaluate side-chains 247 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.123661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.100421 restraints weight = 15631.370| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.72 r_work: 0.2862 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13805 Z= 0.172 Angle : 0.547 7.979 18825 Z= 0.270 Chirality : 0.042 0.148 2290 Planarity : 0.004 0.027 2345 Dihedral : 3.947 15.916 1950 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.91 % Allowed : 17.84 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.88 (0.21), residues: 1720 helix: 2.44 (0.19), residues: 690 sheet: -0.42 (0.24), residues: 520 loop : -0.85 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 248 TYR 0.018 0.002 TYR D 406 PHE 0.015 0.002 PHE A 251 TRP 0.005 0.001 TRP C 88 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00419 (13790) covalent geometry : angle 0.54677 (18790) SS BOND : bond 0.00052 ( 10) SS BOND : angle 0.76171 ( 20) hydrogen bonds : bond 0.04814 ( 761) hydrogen bonds : angle 4.25068 ( 2382) link_NAG-ASN : bond 0.00187 ( 5) link_NAG-ASN : angle 0.87657 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.532 Fit side-chains REVERT: A 56 PHE cc_start: 0.7441 (t80) cc_final: 0.6900 (t80) REVERT: A 263 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7969 (tt) REVERT: B 33 MET cc_start: 0.8179 (ttp) cc_final: 0.7691 (ttm) REVERT: B 259 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7709 (t80) REVERT: B 379 LYS cc_start: 0.7790 (mptt) cc_final: 0.7310 (ttpt) REVERT: B 403 MET cc_start: 0.8139 (ttp) cc_final: 0.7869 (ttp) REVERT: C 379 LYS cc_start: 0.7665 (mptt) cc_final: 0.7256 (ttpt) REVERT: D 56 PHE cc_start: 0.7540 (t80) cc_final: 0.7209 (t80) REVERT: D 259 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7709 (t80) REVERT: D 379 LYS cc_start: 0.7790 (mptt) cc_final: 0.7298 (ttpt) REVERT: E 259 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7678 (t80) REVERT: E 379 LYS cc_start: 0.7813 (mptt) cc_final: 0.7294 (ttpt) REVERT: E 393 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8009 (mm) outliers start: 43 outliers final: 28 residues processed: 243 average time/residue: 0.1176 time to fit residues: 42.8644 Evaluate side-chains 245 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN D 374 HIS E 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.121855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.098466 restraints weight = 15681.719| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.76 r_work: 0.2833 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13805 Z= 0.220 Angle : 0.592 7.757 18825 Z= 0.293 Chirality : 0.044 0.189 2290 Planarity : 0.004 0.027 2345 Dihedral : 4.177 17.092 1950 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.58 % Allowed : 17.77 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.21), residues: 1720 helix: 2.24 (0.19), residues: 690 sheet: -0.55 (0.24), residues: 520 loop : -0.88 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 248 TYR 0.018 0.002 TYR D 406 PHE 0.016 0.002 PHE A 251 TRP 0.006 0.001 TRP E 88 HIS 0.005 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00545 (13790) covalent geometry : angle 0.59163 (18790) SS BOND : bond 0.00034 ( 10) SS BOND : angle 0.89487 ( 20) hydrogen bonds : bond 0.05164 ( 761) hydrogen bonds : angle 4.39061 ( 2382) link_NAG-ASN : bond 0.00310 ( 5) link_NAG-ASN : angle 1.00755 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.560 Fit side-chains REVERT: A 259 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7982 (t80) REVERT: A 263 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 259 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7668 (t80) REVERT: B 379 LYS cc_start: 0.7823 (mptt) cc_final: 0.7333 (ttpt) REVERT: C 379 LYS cc_start: 0.7690 (mptt) cc_final: 0.7261 (ttpt) REVERT: D 56 PHE cc_start: 0.7685 (t80) cc_final: 0.7343 (t80) REVERT: D 259 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7675 (t80) REVERT: D 379 LYS cc_start: 0.7783 (mptt) cc_final: 0.7283 (ttpt) REVERT: E 259 PHE cc_start: 0.8318 (OUTLIER) cc_final: 0.7644 (t80) REVERT: E 379 LYS cc_start: 0.7785 (mptt) cc_final: 0.7269 (ttpt) REVERT: E 393 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8019 (mm) outliers start: 53 outliers final: 35 residues processed: 247 average time/residue: 0.1147 time to fit residues: 42.5941 Evaluate side-chains 253 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.123025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.099720 restraints weight = 15577.271| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.76 r_work: 0.2851 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13805 Z= 0.171 Angle : 0.557 10.536 18825 Z= 0.276 Chirality : 0.042 0.139 2290 Planarity : 0.004 0.030 2345 Dihedral : 4.058 16.643 1950 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.97 % Allowed : 18.85 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.76 (0.21), residues: 1720 helix: 2.38 (0.19), residues: 685 sheet: -0.58 (0.24), residues: 520 loop : -0.81 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 248 TYR 0.017 0.001 TYR D 406 PHE 0.014 0.002 PHE A 251 TRP 0.005 0.001 TRP E 88 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00415 (13790) covalent geometry : angle 0.55358 (18790) SS BOND : bond 0.00173 ( 10) SS BOND : angle 1.96928 ( 20) hydrogen bonds : bond 0.04828 ( 761) hydrogen bonds : angle 4.30126 ( 2382) link_NAG-ASN : bond 0.00153 ( 5) link_NAG-ASN : angle 0.85017 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.538 Fit side-chains REVERT: A 56 PHE cc_start: 0.7515 (t80) cc_final: 0.6910 (t80) REVERT: A 259 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7879 (t80) REVERT: A 263 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7916 (tt) REVERT: B 33 MET cc_start: 0.8168 (ttp) cc_final: 0.7734 (ttm) REVERT: B 259 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 379 LYS cc_start: 0.7787 (mptt) cc_final: 0.7307 (ttpt) REVERT: B 406 TYR cc_start: 0.8026 (t80) cc_final: 0.7739 (t80) REVERT: C 379 LYS cc_start: 0.7637 (mptt) cc_final: 0.7237 (ttpt) REVERT: D 56 PHE cc_start: 0.7628 (t80) cc_final: 0.7252 (t80) REVERT: D 259 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7664 (t80) REVERT: D 379 LYS cc_start: 0.7774 (mptt) cc_final: 0.7285 (ttpt) REVERT: E 259 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7611 (t80) REVERT: E 379 LYS cc_start: 0.7801 (mptt) cc_final: 0.7282 (ttpt) REVERT: E 393 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8023 (mm) outliers start: 44 outliers final: 33 residues processed: 245 average time/residue: 0.1141 time to fit residues: 41.8526 Evaluate side-chains 254 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.124574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.101378 restraints weight = 15598.771| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.75 r_work: 0.2874 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13805 Z= 0.132 Angle : 0.522 10.224 18825 Z= 0.259 Chirality : 0.041 0.135 2290 Planarity : 0.003 0.032 2345 Dihedral : 3.873 15.236 1950 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.64 % Allowed : 19.59 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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 (0.21), residues: 1720 helix: 2.61 (0.19), residues: 685 sheet: -0.56 (0.23), residues: 525 loop : -0.74 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 248 TYR 0.018 0.001 TYR D 406 PHE 0.015 0.001 PHE C 384 TRP 0.005 0.001 TRP D 81 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00311 (13790) covalent geometry : angle 0.51767 (18790) SS BOND : bond 0.00119 ( 10) SS BOND : angle 2.02829 ( 20) hydrogen bonds : bond 0.04417 ( 761) hydrogen bonds : angle 4.14981 ( 2382) link_NAG-ASN : bond 0.00047 ( 5) link_NAG-ASN : angle 0.76606 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.528 Fit side-chains REVERT: A 56 PHE cc_start: 0.7404 (t80) cc_final: 0.6885 (t80) REVERT: A 259 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7816 (t80) REVERT: B 33 MET cc_start: 0.8148 (ttp) cc_final: 0.7727 (ttm) REVERT: B 56 PHE cc_start: 0.7476 (t80) cc_final: 0.7251 (t80) REVERT: B 259 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 379 LYS cc_start: 0.7712 (mptt) cc_final: 0.7310 (ttpt) REVERT: C 379 LYS cc_start: 0.7568 (mptt) cc_final: 0.7246 (ttpt) REVERT: D 56 PHE cc_start: 0.7440 (t80) cc_final: 0.7044 (t80) REVERT: D 259 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7712 (t80) REVERT: D 379 LYS cc_start: 0.7742 (mptt) cc_final: 0.7281 (ttpt) REVERT: E 259 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7629 (t80) REVERT: E 379 LYS cc_start: 0.7787 (mptt) cc_final: 0.7338 (ttpt) REVERT: E 393 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7998 (mm) outliers start: 39 outliers final: 28 residues processed: 246 average time/residue: 0.1083 time to fit residues: 40.6250 Evaluate side-chains 245 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 ASN D 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.124212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.101027 restraints weight = 15650.161| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.72 r_work: 0.2870 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13805 Z= 0.146 Angle : 0.527 6.512 18825 Z= 0.263 Chirality : 0.041 0.137 2290 Planarity : 0.003 0.032 2345 Dihedral : 3.901 15.469 1950 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.91 % Allowed : 19.46 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.96 (0.21), residues: 1720 helix: 2.63 (0.19), residues: 685 sheet: -0.58 (0.23), residues: 525 loop : -0.72 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 248 TYR 0.021 0.001 TYR B 406 PHE 0.014 0.001 PHE C 384 TRP 0.005 0.001 TRP E 88 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00349 (13790) covalent geometry : angle 0.52362 (18790) SS BOND : bond 0.00120 ( 10) SS BOND : angle 1.77666 ( 20) hydrogen bonds : bond 0.04490 ( 761) hydrogen bonds : angle 4.11482 ( 2382) link_NAG-ASN : bond 0.00117 ( 5) link_NAG-ASN : angle 0.83045 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.570 Fit side-chains REVERT: A 56 PHE cc_start: 0.7405 (t80) cc_final: 0.6871 (t80) REVERT: A 259 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7868 (t80) REVERT: B 33 MET cc_start: 0.8150 (ttp) cc_final: 0.7716 (ttm) REVERT: B 56 PHE cc_start: 0.7497 (t80) cc_final: 0.7245 (t80) REVERT: B 259 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7670 (t80) REVERT: B 379 LYS cc_start: 0.7750 (mptt) cc_final: 0.7400 (ttpt) REVERT: C 379 LYS cc_start: 0.7570 (mptt) cc_final: 0.7261 (ttpt) REVERT: D 56 PHE cc_start: 0.7480 (t80) cc_final: 0.7052 (t80) REVERT: D 259 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7748 (t80) REVERT: D 379 LYS cc_start: 0.7747 (mptt) cc_final: 0.7305 (ttpt) REVERT: E 259 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7645 (t80) REVERT: E 263 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7955 (tt) REVERT: E 379 LYS cc_start: 0.7753 (mptt) cc_final: 0.7335 (ttpt) REVERT: E 393 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8029 (mm) outliers start: 43 outliers final: 31 residues processed: 245 average time/residue: 0.1140 time to fit residues: 42.1291 Evaluate side-chains 248 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 134 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.125133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.102077 restraints weight = 15537.263| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.71 r_work: 0.2887 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13805 Z= 0.127 Angle : 0.519 6.475 18825 Z= 0.260 Chirality : 0.041 0.135 2290 Planarity : 0.003 0.032 2345 Dihedral : 3.826 14.593 1950 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.16 % Allowed : 20.34 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.06 (0.21), residues: 1720 helix: 2.74 (0.19), residues: 685 sheet: -0.55 (0.23), residues: 525 loop : -0.69 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 248 TYR 0.020 0.001 TYR D 406 PHE 0.015 0.001 PHE C 384 TRP 0.005 0.001 TRP D 81 HIS 0.003 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00297 (13790) covalent geometry : angle 0.51192 (18790) SS BOND : bond 0.00180 ( 10) SS BOND : angle 2.65504 ( 20) hydrogen bonds : bond 0.04294 ( 761) hydrogen bonds : angle 4.05067 ( 2382) link_NAG-ASN : bond 0.00043 ( 5) link_NAG-ASN : angle 0.74534 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.560 Fit side-chains REVERT: A 56 PHE cc_start: 0.7348 (t80) cc_final: 0.6866 (t80) REVERT: A 259 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 33 MET cc_start: 0.8145 (ttp) cc_final: 0.7725 (ttm) REVERT: B 56 PHE cc_start: 0.7438 (t80) cc_final: 0.7188 (t80) REVERT: B 259 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7646 (t80) REVERT: B 379 LYS cc_start: 0.7701 (mptt) cc_final: 0.7339 (ttpt) REVERT: C 379 LYS cc_start: 0.7624 (mptt) cc_final: 0.7297 (ttpt) REVERT: D 56 PHE cc_start: 0.7384 (t80) cc_final: 0.6987 (t80) REVERT: D 259 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7778 (t80) REVERT: D 379 LYS cc_start: 0.7719 (mptt) cc_final: 0.7302 (ttpt) REVERT: E 259 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7655 (t80) REVERT: E 263 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7987 (tt) REVERT: E 379 LYS cc_start: 0.7727 (mptt) cc_final: 0.7319 (ttpt) outliers start: 32 outliers final: 23 residues processed: 239 average time/residue: 0.1083 time to fit residues: 39.7636 Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.125904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.102837 restraints weight = 15591.281| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.72 r_work: 0.2897 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13805 Z= 0.117 Angle : 0.507 6.457 18825 Z= 0.254 Chirality : 0.040 0.136 2290 Planarity : 0.003 0.029 2345 Dihedral : 3.752 13.989 1950 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.09 % Allowed : 20.61 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.14 (0.21), residues: 1720 helix: 2.85 (0.19), residues: 685 sheet: -0.54 (0.23), residues: 525 loop : -0.66 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 74 TYR 0.022 0.001 TYR B 406 PHE 0.015 0.001 PHE E 384 TRP 0.005 0.001 TRP D 81 HIS 0.003 0.001 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00270 (13790) covalent geometry : angle 0.50057 (18790) SS BOND : bond 0.00171 ( 10) SS BOND : angle 2.41894 ( 20) hydrogen bonds : bond 0.04140 ( 761) hydrogen bonds : angle 3.97764 ( 2382) link_NAG-ASN : bond 0.00014 ( 5) link_NAG-ASN : angle 0.73887 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2981.82 seconds wall clock time: 52 minutes 5.14 seconds (3125.14 seconds total)