Starting phenix.real_space_refine on Wed Jun 11 21:45:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wge_37511/06_2025/8wge_37511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wge_37511/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wge_37511/06_2025/8wge_37511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wge_37511/06_2025/8wge_37511.map" model { file = "/net/cci-nas-00/data/ceres_data/8wge_37511/06_2025/8wge_37511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wge_37511/06_2025/8wge_37511.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4} 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: 8.94, per 1000 atoms: 0.66 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: 3.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.51 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: 4.57 Time building geometry restraints manager: 3.88 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: 0.03 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: 1.120 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.190 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- 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 : 6.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 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 TRP 0.003 0.000 TRP D 192 HIS 0.008 0.000 HIS A 374 PHE 0.019 0.001 PHE E 385 TYR 0.012 0.001 TYR E 59 ARG 0.002 0.000 ARG C 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 5) link_NAG-ASN : angle 0.59979 ( 15) hydrogen bonds : bond 0.21034 ( 761) hydrogen bonds : angle 6.72131 ( 2382) SS BOND : bond 0.00112 ( 10) SS BOND : angle 0.52304 ( 20) covalent geometry : bond 0.00214 (13790) covalent geometry : angle 0.44413 (18790) *********************** 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 : 1.569 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: 0.2385 time to fit residues: 85.9900 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 : 1.571 ------------------------------------------------------------------------------- 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 143 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.121191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.097502 restraints weight = 15585.512| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.88 r_work: 0.2821 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13805 Z= 0.223 Angle : 0.600 7.988 18825 Z= 0.303 Chirality : 0.044 0.145 2290 Planarity : 0.004 0.032 2345 Dihedral : 4.314 24.483 1953 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.36 % Allowed : 15.54 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1720 helix: 2.14 (0.19), residues: 690 sheet: -0.19 (0.24), residues: 520 loop : -0.90 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 88 HIS 0.005 0.001 HIS A 283 PHE 0.017 0.002 PHE A 251 TYR 0.017 0.002 TYR D 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 1.02531 ( 15) hydrogen bonds : bond 0.05859 ( 761) hydrogen bonds : angle 4.66941 ( 2382) SS BOND : bond 0.00098 ( 10) SS BOND : angle 0.98845 ( 20) covalent geometry : bond 0.00547 (13790) covalent geometry : angle 0.59911 (18790) *********************** 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: 35 poor density : 218 time to evaluate : 1.603 Fit side-chains REVERT: A 56 PHE cc_start: 0.7786 (t80) cc_final: 0.7437 (t80) REVERT: B 33 MET cc_start: 0.8135 (ttp) cc_final: 0.7677 (ttm) REVERT: B 42 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7342 (ptm) REVERT: C 127 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8850 (pp) REVERT: C 222 MET cc_start: 0.7739 (mtp) cc_final: 0.7421 (mtt) REVERT: C 403 MET cc_start: 0.8082 (ttp) cc_final: 0.7865 (ttp) REVERT: D 127 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8800 (pp) REVERT: E 259 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7575 (t80) REVERT: E 379 LYS cc_start: 0.7808 (mptt) cc_final: 0.7162 (ttpt) outliers start: 35 outliers final: 26 residues processed: 236 average time/residue: 0.2326 time to fit residues: 82.5492 Evaluate side-chains 242 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 165 ILE 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 42 MET Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 165 ILE 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 393 LEU Chi-restraints excluded: chain C residue 127 LEU 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 D residue 90 THR Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 127 LEU 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.103732 restraints weight = 15572.451| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.68 r_work: 0.2911 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13805 Z= 0.105 Angle : 0.479 7.036 18825 Z= 0.241 Chirality : 0.040 0.133 2290 Planarity : 0.003 0.030 2345 Dihedral : 3.658 13.229 1950 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.43 % Allowed : 16.15 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1720 helix: 2.66 (0.19), residues: 685 sheet: -0.21 (0.24), residues: 525 loop : -0.82 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.002 0.001 HIS E 283 PHE 0.015 0.001 PHE C 384 TYR 0.011 0.001 TYR D 406 ARG 0.002 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 5) link_NAG-ASN : angle 0.76324 ( 15) hydrogen bonds : bond 0.04457 ( 761) hydrogen bonds : angle 4.14770 ( 2382) SS BOND : bond 0.00107 ( 10) SS BOND : angle 0.50637 ( 20) covalent geometry : bond 0.00229 (13790) covalent geometry : angle 0.47907 (18790) *********************** 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 269 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 1.458 Fit side-chains REVERT: A 56 PHE cc_start: 0.7343 (t80) cc_final: 0.7064 (t80) REVERT: B 33 MET cc_start: 0.8059 (ttp) cc_final: 0.7655 (ttm) REVERT: B 36 ASP cc_start: 0.7703 (m-30) cc_final: 0.7420 (m-30) REVERT: B 127 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8836 (pp) REVERT: B 259 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7642 (t80) REVERT: C 33 MET cc_start: 0.8188 (ttp) cc_final: 0.7553 (ttm) REVERT: C 127 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8952 (pp) REVERT: D 56 PHE cc_start: 0.7341 (t80) cc_final: 0.7031 (t80) REVERT: D 259 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7602 (t80) REVERT: E 259 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7567 (t80) REVERT: E 393 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7889 (mm) outliers start: 36 outliers final: 14 residues processed: 259 average time/residue: 0.2080 time to fit residues: 83.8604 Evaluate side-chains 238 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 393 LEU 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 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 D residue 99 MET Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 174 VAL 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.123807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.100552 restraints weight = 15428.176| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.74 r_work: 0.2864 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13805 Z= 0.165 Angle : 0.549 8.711 18825 Z= 0.269 Chirality : 0.042 0.139 2290 Planarity : 0.004 0.028 2345 Dihedral : 3.885 14.770 1950 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.77 % Allowed : 16.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1720 helix: 2.53 (0.19), residues: 690 sheet: -0.21 (0.24), residues: 510 loop : -0.71 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 88 HIS 0.004 0.001 HIS A 283 PHE 0.015 0.002 PHE A 251 TYR 0.016 0.002 TYR D 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 5) link_NAG-ASN : angle 0.91689 ( 15) hydrogen bonds : bond 0.04826 ( 761) hydrogen bonds : angle 4.24774 ( 2382) SS BOND : bond 0.00055 ( 10) SS BOND : angle 0.75958 ( 20) covalent geometry : bond 0.00400 (13790) covalent geometry : angle 0.54787 (18790) *********************** 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 255 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 1.567 Fit side-chains REVERT: A 56 PHE cc_start: 0.7430 (t80) cc_final: 0.6932 (t80) REVERT: A 259 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7874 (t80) REVERT: B 33 MET cc_start: 0.8173 (ttp) cc_final: 0.7700 (ttm) REVERT: B 259 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 379 LYS cc_start: 0.7780 (mptt) cc_final: 0.7276 (ttpt) REVERT: B 403 MET cc_start: 0.8151 (ttp) cc_final: 0.7927 (ttp) REVERT: C 127 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8896 (pp) REVERT: C 379 LYS cc_start: 0.7681 (mptt) cc_final: 0.7228 (ttpt) REVERT: D 56 PHE cc_start: 0.7514 (t80) cc_final: 0.7151 (t80) REVERT: D 259 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7677 (t80) REVERT: D 379 LYS cc_start: 0.7759 (mptt) cc_final: 0.7254 (ttpt) REVERT: E 259 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7626 (t80) REVERT: E 379 LYS cc_start: 0.7791 (mptt) cc_final: 0.7236 (ttpt) REVERT: E 393 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7928 (mm) outliers start: 41 outliers final: 27 residues processed: 240 average time/residue: 0.2317 time to fit residues: 84.0341 Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 259 PHE Chi-restraints excluded: chain A residue 393 LEU 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 386 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 127 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 386 LEU Chi-restraints excluded: chain C residue 404 VAL 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 404 VAL Chi-restraints excluded: chain E residue 57 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.125364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.102156 restraints weight = 15514.633| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.74 r_work: 0.2882 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13805 Z= 0.130 Angle : 0.504 7.616 18825 Z= 0.249 Chirality : 0.040 0.132 2290 Planarity : 0.003 0.027 2345 Dihedral : 3.749 14.491 1950 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.64 % Allowed : 18.24 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1720 helix: 2.69 (0.19), residues: 685 sheet: -0.35 (0.24), residues: 525 loop : -0.77 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 81 HIS 0.003 0.001 HIS A 283 PHE 0.015 0.001 PHE C 384 TYR 0.016 0.001 TYR D 406 ARG 0.001 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 5) link_NAG-ASN : angle 0.75348 ( 15) hydrogen bonds : bond 0.04415 ( 761) hydrogen bonds : angle 4.08852 ( 2382) SS BOND : bond 0.00068 ( 10) SS BOND : angle 0.62612 ( 20) covalent geometry : bond 0.00306 (13790) covalent geometry : angle 0.50336 (18790) *********************** 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 258 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 1.475 Fit side-chains REVERT: A 56 PHE cc_start: 0.7326 (t80) cc_final: 0.6862 (t80) REVERT: A 259 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 33 MET cc_start: 0.8079 (ttp) cc_final: 0.7637 (ttm) REVERT: B 36 ASP cc_start: 0.7595 (m-30) cc_final: 0.7316 (m-30) REVERT: B 42 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7462 (ptm) REVERT: B 56 PHE cc_start: 0.7353 (t80) cc_final: 0.7152 (t80) REVERT: B 85 GLN cc_start: 0.8421 (mp10) cc_final: 0.8199 (mp10) REVERT: B 259 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7636 (t80) REVERT: B 379 LYS cc_start: 0.7738 (mptt) cc_final: 0.7308 (ttpt) REVERT: B 406 TYR cc_start: 0.8007 (t80) cc_final: 0.7677 (t80) REVERT: C 127 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8951 (pp) REVERT: C 259 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7672 (t80) REVERT: C 379 LYS cc_start: 0.7597 (mptt) cc_final: 0.7242 (ttpt) REVERT: D 56 PHE cc_start: 0.7384 (t80) cc_final: 0.7023 (t80) REVERT: D 259 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7660 (t80) REVERT: D 276 CYS cc_start: 0.6902 (m) cc_final: 0.5972 (p) REVERT: D 379 LYS cc_start: 0.7719 (mptt) cc_final: 0.7278 (ttpt) REVERT: E 33 MET cc_start: 0.8101 (ttp) cc_final: 0.7491 (ttm) REVERT: E 259 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7659 (t80) REVERT: E 379 LYS cc_start: 0.7773 (mptt) cc_final: 0.7266 (ttpt) REVERT: E 393 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8020 (mm) outliers start: 39 outliers final: 24 residues processed: 245 average time/residue: 0.2183 time to fit residues: 81.8041 Evaluate side-chains 249 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 42 MET 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 386 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 111 GLN 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 386 LEU Chi-restraints excluded: chain C residue 404 VAL 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 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 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 132 optimal weight: 20.0000 chunk 3 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.122179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.098931 restraints weight = 15737.657| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.73 r_work: 0.2840 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13805 Z= 0.214 Angle : 0.586 8.524 18825 Z= 0.289 Chirality : 0.043 0.140 2290 Planarity : 0.004 0.029 2345 Dihedral : 4.093 16.660 1950 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.04 % Allowed : 18.65 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1720 helix: 2.33 (0.19), residues: 690 sheet: -0.50 (0.24), residues: 520 loop : -0.87 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 88 HIS 0.005 0.001 HIS A 283 PHE 0.016 0.002 PHE A 251 TYR 0.021 0.002 TYR D 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 5) link_NAG-ASN : angle 0.98253 ( 15) hydrogen bonds : bond 0.05072 ( 761) hydrogen bonds : angle 4.31685 ( 2382) SS BOND : bond 0.00037 ( 10) SS BOND : angle 0.90378 ( 20) covalent geometry : bond 0.00530 (13790) covalent geometry : angle 0.58486 (18790) *********************** 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 261 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.591 Fit side-chains REVERT: A 259 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7880 (t80) REVERT: B 259 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7652 (t80) REVERT: B 379 LYS cc_start: 0.7790 (mptt) cc_final: 0.7324 (ttpt) REVERT: B 406 TYR cc_start: 0.8023 (t80) cc_final: 0.7755 (t80) REVERT: C 127 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8901 (pp) REVERT: C 379 LYS cc_start: 0.7660 (mptt) cc_final: 0.7252 (ttpt) REVERT: D 56 PHE cc_start: 0.7649 (t80) cc_final: 0.7277 (t80) REVERT: D 379 LYS cc_start: 0.7776 (mptt) cc_final: 0.7308 (ttpt) REVERT: E 379 LYS cc_start: 0.7812 (mptt) cc_final: 0.7289 (ttpt) outliers start: 45 outliers final: 30 residues processed: 245 average time/residue: 0.2370 time to fit residues: 86.7874 Evaluate side-chains 246 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 259 PHE 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 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 57 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 127 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 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 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 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 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN E 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.125397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.102123 restraints weight = 15532.110| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.75 r_work: 0.2883 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1741 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= 0.118 Angle : 0.506 10.721 18825 Z= 0.251 Chirality : 0.040 0.131 2290 Planarity : 0.003 0.029 2345 Dihedral : 3.780 14.511 1950 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.36 % Allowed : 19.39 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1720 helix: 2.68 (0.19), residues: 685 sheet: -0.48 (0.24), residues: 525 loop : -0.74 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 81 HIS 0.003 0.001 HIS A 283 PHE 0.015 0.001 PHE C 384 TYR 0.016 0.001 TYR D 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 5) link_NAG-ASN : angle 0.69829 ( 15) hydrogen bonds : bond 0.04328 ( 761) hydrogen bonds : angle 4.07450 ( 2382) SS BOND : bond 0.00097 ( 10) SS BOND : angle 1.51542 ( 20) covalent geometry : bond 0.00271 (13790) covalent geometry : angle 0.50342 (18790) *********************** 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 256 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.455 Fit side-chains REVERT: A 56 PHE cc_start: 0.7364 (t80) cc_final: 0.6841 (t80) REVERT: A 259 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7719 (t80) REVERT: B 33 MET cc_start: 0.8095 (ttp) cc_final: 0.7685 (ttm) REVERT: B 36 ASP cc_start: 0.7645 (m-30) cc_final: 0.7406 (m-30) REVERT: B 56 PHE cc_start: 0.7408 (t80) cc_final: 0.7185 (t80) REVERT: B 259 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 379 LYS cc_start: 0.7708 (mptt) cc_final: 0.7307 (ttpt) REVERT: C 127 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8931 (pp) REVERT: C 379 LYS cc_start: 0.7581 (mptt) cc_final: 0.7271 (ttpt) REVERT: D 56 PHE cc_start: 0.7378 (t80) cc_final: 0.7006 (t80) REVERT: D 259 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7683 (t80) REVERT: D 379 LYS cc_start: 0.7709 (mptt) cc_final: 0.7279 (ttpt) REVERT: E 379 LYS cc_start: 0.7772 (mptt) cc_final: 0.7315 (ttpt) REVERT: E 393 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7967 (mm) outliers start: 35 outliers final: 26 residues processed: 246 average time/residue: 0.2371 time to fit residues: 87.1705 Evaluate side-chains 246 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET 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 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 B residue 386 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 103 ASP 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 99 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 259 PHE Chi-restraints excluded: chain D residue 393 LEU 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 73 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.122891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.099669 restraints weight = 15633.531| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.72 r_work: 0.2850 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1791 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= 0.193 Angle : 0.570 7.099 18825 Z= 0.283 Chirality : 0.043 0.138 2290 Planarity : 0.004 0.030 2345 Dihedral : 4.050 16.810 1950 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.91 % Allowed : 19.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1720 helix: 2.42 (0.19), residues: 690 sheet: -0.56 (0.24), residues: 520 loop : -0.80 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 88 HIS 0.004 0.001 HIS A 283 PHE 0.015 0.002 PHE B 236 TYR 0.023 0.002 TYR D 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 5) link_NAG-ASN : angle 0.92723 ( 15) hydrogen bonds : bond 0.04871 ( 761) hydrogen bonds : angle 4.25974 ( 2382) SS BOND : bond 0.00205 ( 10) SS BOND : angle 1.89957 ( 20) covalent geometry : bond 0.00475 (13790) covalent geometry : angle 0.56686 (18790) *********************** 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 247 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 1.357 Fit side-chains REVERT: A 259 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7738 (t80) REVERT: A 400 LEU cc_start: 0.7832 (mm) cc_final: 0.7305 (mt) REVERT: B 33 MET cc_start: 0.8177 (ttp) cc_final: 0.7722 (ttm) REVERT: B 259 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7664 (t80) REVERT: B 379 LYS cc_start: 0.7750 (mptt) cc_final: 0.7322 (ttpt) REVERT: C 127 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8896 (pp) REVERT: C 379 LYS cc_start: 0.7644 (mptt) cc_final: 0.7294 (ttpt) REVERT: D 56 PHE cc_start: 0.7593 (t80) cc_final: 0.7247 (t80) REVERT: D 259 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7666 (t80) REVERT: D 379 LYS cc_start: 0.7768 (mptt) cc_final: 0.7308 (ttpt) REVERT: E 379 LYS cc_start: 0.7814 (mptt) cc_final: 0.7353 (ttpt) REVERT: E 393 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8048 (mm) outliers start: 43 outliers final: 32 residues processed: 233 average time/residue: 0.2684 time to fit residues: 94.5254 Evaluate side-chains 240 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 B residue 402 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 127 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 266 LEU 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 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 404 VAL Chi-restraints excluded: chain E residue 57 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.125791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.102482 restraints weight = 15533.082| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.75 r_work: 0.2890 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13805 Z= 0.114 Angle : 0.501 6.405 18825 Z= 0.250 Chirality : 0.040 0.132 2290 Planarity : 0.003 0.032 2345 Dihedral : 3.768 14.213 1950 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 20.54 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.21), residues: 1720 helix: 2.77 (0.19), residues: 685 sheet: -0.48 (0.23), residues: 525 loop : -0.68 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 81 HIS 0.003 0.001 HIS A 283 PHE 0.015 0.001 PHE C 384 TYR 0.020 0.001 TYR B 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00011 ( 5) link_NAG-ASN : angle 0.69974 ( 15) hydrogen bonds : bond 0.04212 ( 761) hydrogen bonds : angle 4.03444 ( 2382) SS BOND : bond 0.00104 ( 10) SS BOND : angle 2.17253 ( 20) covalent geometry : bond 0.00260 (13790) covalent geometry : angle 0.49630 (18790) *********************** 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 242 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 1.690 Fit side-chains REVERT: A 56 PHE cc_start: 0.7346 (t80) cc_final: 0.6838 (t80) REVERT: A 259 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7624 (t80) REVERT: B 33 MET cc_start: 0.8075 (ttp) cc_final: 0.7664 (ttm) REVERT: B 36 ASP cc_start: 0.7640 (m-30) cc_final: 0.7389 (m-30) REVERT: B 56 PHE cc_start: 0.7414 (t80) cc_final: 0.7162 (t80) REVERT: B 85 GLN cc_start: 0.8357 (mp10) cc_final: 0.8149 (mp10) REVERT: B 259 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7667 (t80) REVERT: B 263 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7897 (tt) REVERT: B 379 LYS cc_start: 0.7681 (mptt) cc_final: 0.7287 (ttpt) REVERT: C 379 LYS cc_start: 0.7599 (mptt) cc_final: 0.7265 (ttpt) REVERT: D 56 PHE cc_start: 0.7347 (t80) cc_final: 0.6955 (t80) REVERT: D 259 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7686 (t80) REVERT: D 276 CYS cc_start: 0.6802 (m) cc_final: 0.5915 (p) REVERT: D 379 LYS cc_start: 0.7645 (mptt) cc_final: 0.7241 (ttpt) REVERT: E 259 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7631 (t80) REVERT: E 379 LYS cc_start: 0.7696 (mptt) cc_final: 0.7286 (ttpt) REVERT: E 393 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7990 (mm) outliers start: 31 outliers final: 21 residues processed: 234 average time/residue: 0.2707 time to fit residues: 98.6907 Evaluate side-chains 235 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 259 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS 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 263 LEU 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8111 > 50: distance: 22 - 113: 6.311 distance: 48 - 52: 19.009 distance: 52 - 53: 9.700 distance: 53 - 54: 26.216 distance: 53 - 56: 35.102 distance: 54 - 55: 44.146 distance: 54 - 64: 26.693 distance: 56 - 57: 17.263 distance: 57 - 58: 10.696 distance: 57 - 59: 16.970 distance: 58 - 60: 28.490 distance: 59 - 61: 35.184 distance: 60 - 62: 38.297 distance: 61 - 62: 33.598 distance: 62 - 63: 18.895 distance: 64 - 65: 23.941 distance: 64 - 70: 26.333 distance: 65 - 66: 37.063 distance: 65 - 68: 8.776 distance: 66 - 67: 43.204 distance: 66 - 71: 23.334 distance: 68 - 69: 14.756 distance: 69 - 70: 37.698 distance: 71 - 72: 32.455 distance: 72 - 73: 21.831 distance: 72 - 75: 19.095 distance: 73 - 74: 6.148 distance: 73 - 82: 29.234 distance: 75 - 76: 12.423 distance: 76 - 77: 11.601 distance: 76 - 78: 10.093 distance: 77 - 79: 17.155 distance: 78 - 80: 21.604 distance: 80 - 81: 11.639 distance: 82 - 83: 19.618 distance: 83 - 84: 11.656 distance: 83 - 86: 19.271 distance: 84 - 85: 26.560 distance: 84 - 87: 24.256 distance: 87 - 88: 16.068 distance: 88 - 89: 19.291 distance: 89 - 90: 33.991 distance: 89 - 91: 9.158 distance: 91 - 92: 12.623 distance: 91 - 181: 19.952 distance: 92 - 93: 47.004 distance: 92 - 95: 24.713 distance: 93 - 94: 10.572 distance: 93 - 99: 58.811 distance: 94 - 178: 32.371 distance: 95 - 96: 30.380 distance: 96 - 97: 39.690 distance: 96 - 98: 18.161 distance: 99 - 100: 44.180 distance: 100 - 101: 37.046 distance: 100 - 103: 30.394 distance: 101 - 102: 23.536 distance: 101 - 108: 11.547 distance: 103 - 104: 33.247 distance: 104 - 105: 27.203 distance: 105 - 106: 34.368 distance: 105 - 107: 15.143 distance: 108 - 109: 16.481 distance: 108 - 171: 18.150 distance: 109 - 110: 7.370 distance: 109 - 112: 14.228 distance: 110 - 111: 13.370 distance: 110 - 114: 16.728 distance: 111 - 168: 13.182 distance: 112 - 113: 12.332 distance: 114 - 115: 14.312 distance: 114 - 120: 9.385 distance: 115 - 116: 9.575 distance: 115 - 118: 7.488 distance: 116 - 117: 6.449 distance: 116 - 121: 8.378 distance: 118 - 119: 17.379 distance: 119 - 120: 18.449 distance: 121 - 122: 7.840 distance: 121 - 159: 11.875 distance: 122 - 123: 25.556 distance: 122 - 125: 7.067 distance: 123 - 124: 27.493 distance: 123 - 128: 24.504 distance: 124 - 156: 6.009 distance: 125 - 126: 16.619 distance: 125 - 127: 8.117