Starting phenix.real_space_refine on Thu May 15 14:33:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wge_37511/05_2025/8wge_37511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wge_37511/05_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_37511/05_2025/8wge_37511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wge_37511/05_2025/8wge_37511.map" model { file = "/net/cci-nas-00/data/ceres_data/8wge_37511/05_2025/8wge_37511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wge_37511/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 8.97, 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: 3.39 Conformation dependent library (CDL) restraints added in 2.0 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: 1.78 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: 4.58 Time building geometry restraints manager: 3.99 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: 1.970 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: 1.130 Check model and map are aligned: 0.200 Set scattering table: 0.210 Process input model: 34.440 Find NCS groups from input model: 0.580 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- 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 : 1.492 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: 0.2290 time to fit residues: 82.4800 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 : 1.646 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.097498 restraints weight = 15585.512| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.88 r_work: 0.2823 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 1.625 Fit side-chains REVERT: A 56 PHE cc_start: 0.7786 (t80) cc_final: 0.7437 (t80) REVERT: B 33 MET cc_start: 0.8133 (ttp) cc_final: 0.7676 (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: 0.8851 (pp) REVERT: C 222 MET cc_start: 0.7739 (mtp) cc_final: 0.7421 (mtt) REVERT: C 403 MET cc_start: 0.8083 (ttp) cc_final: 0.7867 (ttp) REVERT: D 127 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8800 (pp) REVERT: E 259 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7576 (t80) REVERT: E 379 LYS cc_start: 0.7805 (mptt) cc_final: 0.7160 (ttpt) outliers start: 35 outliers final: 26 residues processed: 236 average time/residue: 0.2315 time to fit residues: 81.7829 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 : 1.433 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.126087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.103716 restraints weight = 15583.157| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.68 r_work: 0.2915 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1405 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= 0.103 Angle : 0.479 7.038 18825 Z= 0.241 Chirality : 0.039 0.131 2290 Planarity : 0.003 0.030 2345 Dihedral : 3.671 13.215 1950 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 2.67 (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 0.010 0.001 TYR D 406 ARG 0.002 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00060 ( 5) link_NAG-ASN : angle 0.73602 ( 15) hydrogen bonds : bond 0.04482 ( 761) hydrogen bonds : angle 4.16006 ( 2382) SS BOND : bond 0.00103 ( 10) SS BOND : angle 0.49750 ( 20) covalent geometry : bond 0.00220 (13790) covalent geometry : angle 0.47915 (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 268 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 1.552 Fit side-chains REVERT: A 56 PHE cc_start: 0.7366 (t80) cc_final: 0.7079 (t80) REVERT: B 33 MET cc_start: 0.8058 (ttp) cc_final: 0.7650 (ttm) REVERT: B 36 ASP cc_start: 0.7749 (m-30) cc_final: 0.7456 (m-30) REVERT: B 127 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8852 (pp) REVERT: B 259 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7653 (t80) REVERT: C 33 MET cc_start: 0.8199 (ttp) cc_final: 0.7558 (ttm) REVERT: C 127 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8954 (pp) REVERT: D 56 PHE cc_start: 0.7345 (t80) cc_final: 0.7033 (t80) REVERT: D 259 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7602 (t80) REVERT: E 259 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7576 (t80) REVERT: E 393 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7908 (mm) outliers start: 36 outliers final: 15 residues processed: 258 average time/residue: 0.2105 time to fit residues: 83.8320 Evaluate side-chains 239 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 B residue 393 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: 5.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.121094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.097953 restraints weight = 15569.805| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.71 r_work: 0.2831 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13805 Z= 0.260 Angle : 0.639 8.651 18825 Z= 0.314 Chirality : 0.045 0.147 2290 Planarity : 0.004 0.029 2345 Dihedral : 4.272 17.154 1950 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.18 % Allowed : 16.76 % Favored : 80.07 % 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: 0.74 (0.21), residues: 1720 helix: 2.15 (0.19), residues: 690 sheet: -0.38 (0.24), residues: 510 loop : -0.78 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 88 HIS 0.005 0.001 HIS A 283 PHE 0.017 0.002 PHE A 251 TYR 0.018 0.002 TYR D 406 ARG 0.003 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 5) link_NAG-ASN : angle 1.10613 ( 15) hydrogen bonds : bond 0.05536 ( 761) hydrogen bonds : angle 4.50441 ( 2382) SS BOND : bond 0.00053 ( 10) SS BOND : angle 1.02204 ( 20) covalent geometry : bond 0.00648 (13790) covalent geometry : angle 0.63798 (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 262 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 1.608 Fit side-chains REVERT: A 259 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7998 (t80) REVERT: B 39 MET cc_start: 0.8569 (mmt) cc_final: 0.8353 (mmt) REVERT: B 259 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 379 LYS cc_start: 0.7902 (mptt) cc_final: 0.7346 (ttpt) REVERT: B 403 MET cc_start: 0.8155 (ttp) cc_final: 0.7919 (ttp) REVERT: C 379 LYS cc_start: 0.7799 (mptt) cc_final: 0.7290 (ttpt) REVERT: D 379 LYS cc_start: 0.7835 (mptt) cc_final: 0.7294 (ttpt) REVERT: D 403 MET cc_start: 0.8224 (ttp) cc_final: 0.7987 (ttp) REVERT: E 259 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7636 (t80) REVERT: E 379 LYS cc_start: 0.7851 (mptt) cc_final: 0.7276 (ttpt) outliers start: 47 outliers final: 32 residues processed: 240 average time/residue: 0.2345 time to fit residues: 83.0703 Evaluate side-chains 245 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 393 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.102265 restraints weight = 15511.412| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.74 r_work: 0.2890 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13805 Z= 0.117 Angle : 0.503 8.933 18825 Z= 0.249 Chirality : 0.040 0.160 2290 Planarity : 0.003 0.028 2345 Dihedral : 3.791 14.377 1950 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.30 % Allowed : 18.65 % Favored : 79.05 % 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: 1.01 (0.21), residues: 1720 helix: 2.62 (0.19), residues: 685 sheet: -0.39 (0.24), residues: 520 loop : -0.80 (0.26), residues: 515 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 0.016 0.001 PHE C 384 TYR 0.012 0.001 TYR D 406 ARG 0.002 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 5) link_NAG-ASN : angle 0.68201 ( 15) hydrogen bonds : bond 0.04404 ( 761) hydrogen bonds : angle 4.12408 ( 2382) SS BOND : bond 0.00090 ( 10) SS BOND : angle 0.56404 ( 20) covalent geometry : bond 0.00266 (13790) covalent geometry : angle 0.50265 (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 257 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.811 Fit side-chains REVERT: A 56 PHE cc_start: 0.7380 (t80) cc_final: 0.6897 (t80) REVERT: A 259 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7772 (t80) REVERT: B 33 MET cc_start: 0.8093 (ttp) cc_final: 0.7676 (ttm) REVERT: B 56 PHE cc_start: 0.7462 (t80) cc_final: 0.7229 (t80) REVERT: B 259 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7695 (t80) REVERT: B 379 LYS cc_start: 0.7760 (mptt) cc_final: 0.7303 (ttpt) REVERT: C 259 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7682 (t80) REVERT: C 379 LYS cc_start: 0.7635 (mptt) cc_final: 0.7238 (ttpt) REVERT: D 56 PHE cc_start: 0.7463 (t80) cc_final: 0.7172 (t80) REVERT: D 259 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7695 (t80) REVERT: D 379 LYS cc_start: 0.7723 (mptt) cc_final: 0.7261 (ttpt) REVERT: E 33 MET cc_start: 0.8076 (ttp) cc_final: 0.7467 (ttm) REVERT: E 259 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7652 (t80) REVERT: E 379 LYS cc_start: 0.7739 (mptt) cc_final: 0.7261 (ttpt) REVERT: E 393 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7954 (mm) outliers start: 34 outliers final: 19 residues processed: 248 average time/residue: 0.2264 time to fit residues: 84.2803 Evaluate side-chains 242 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 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 393 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 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 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3226 r_free = 0.3226 target = 0.120280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.097011 restraints weight = 15863.812| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.73 r_work: 0.2815 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 13805 Z= 0.285 Angle : 0.643 7.929 18825 Z= 0.320 Chirality : 0.045 0.146 2290 Planarity : 0.004 0.032 2345 Dihedral : 4.348 18.133 1950 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.38 % Allowed : 17.97 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.20), residues: 1720 helix: 2.06 (0.19), residues: 690 sheet: -0.50 (0.24), residues: 510 loop : -0.79 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 88 HIS 0.005 0.001 HIS A 283 PHE 0.017 0.002 PHE A 251 TYR 0.021 0.002 TYR D 406 ARG 0.003 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 1.10969 ( 15) hydrogen bonds : bond 0.05514 ( 761) hydrogen bonds : angle 4.49013 ( 2382) SS BOND : bond 0.00041 ( 10) SS BOND : angle 1.06161 ( 20) covalent geometry : bond 0.00711 (13790) covalent geometry : angle 0.64210 (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 257 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 1.566 Fit side-chains REVERT: A 259 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7921 (t80) REVERT: B 259 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7676 (t80) REVERT: B 379 LYS cc_start: 0.7870 (mptt) cc_final: 0.7334 (ttpt) REVERT: B 406 TYR cc_start: 0.8208 (t80) cc_final: 0.7946 (t80) REVERT: C 379 LYS cc_start: 0.7716 (mptt) cc_final: 0.7263 (ttpt) REVERT: D 259 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7694 (t80) REVERT: D 379 LYS cc_start: 0.7837 (mptt) cc_final: 0.7310 (ttpt) REVERT: E 379 LYS cc_start: 0.7858 (mptt) cc_final: 0.7296 (ttpt) outliers start: 50 outliers final: 37 residues processed: 240 average time/residue: 0.2435 time to fit residues: 86.1162 Evaluate side-chains 239 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 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 259 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 393 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 165 ILE Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 259 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 111 GLN Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 285 CYS Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 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: 0.7980 chunk 137 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 115 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 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 = 0.3301 r_free = 0.3301 target = 0.126578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.103656 restraints weight = 15558.565| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.71 r_work: 0.2905 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13805 Z= 0.104 Angle : 0.494 10.269 18825 Z= 0.247 Chirality : 0.040 0.133 2290 Planarity : 0.003 0.029 2345 Dihedral : 3.735 13.726 1950 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.09 % Allowed : 19.93 % Favored : 77.97 % 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: 1.02 (0.21), residues: 1720 helix: 2.62 (0.19), residues: 690 sheet: -0.48 (0.24), residues: 525 loop : -0.71 (0.27), residues: 505 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 0.016 0.001 PHE C 384 TYR 0.014 0.001 TYR D 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 0.59678 ( 15) hydrogen bonds : bond 0.04140 ( 761) hydrogen bonds : angle 4.04160 ( 2382) SS BOND : bond 0.00114 ( 10) SS BOND : angle 1.35902 ( 20) covalent geometry : bond 0.00227 (13790) covalent geometry : angle 0.49250 (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 253 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 1.476 Fit side-chains REVERT: A 56 PHE cc_start: 0.7283 (t80) cc_final: 0.6802 (t80) REVERT: A 259 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7610 (t80) REVERT: B 33 MET cc_start: 0.8030 (ttp) cc_final: 0.7639 (ttm) REVERT: B 36 ASP cc_start: 0.7623 (m-30) cc_final: 0.7358 (m-30) REVERT: B 56 PHE cc_start: 0.7423 (t80) cc_final: 0.7175 (t80) REVERT: B 259 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7710 (t80) REVERT: B 379 LYS cc_start: 0.7754 (mptt) cc_final: 0.7360 (ttpt) REVERT: C 259 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7715 (t80) REVERT: C 379 LYS cc_start: 0.7617 (mptt) cc_final: 0.7297 (ttpt) REVERT: D 56 PHE cc_start: 0.7374 (t80) cc_final: 0.7139 (t80) REVERT: D 259 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7692 (t80) REVERT: D 276 CYS cc_start: 0.6849 (m) cc_final: 0.5914 (p) REVERT: D 379 LYS cc_start: 0.7729 (mptt) cc_final: 0.7293 (ttpt) REVERT: E 259 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7624 (t80) REVERT: E 393 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8004 (mm) outliers start: 31 outliers final: 17 residues processed: 242 average time/residue: 0.2098 time to fit residues: 77.6144 Evaluate side-chains 238 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 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 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 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 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=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: 4.9990 chunk 44 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 142 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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 = 0.3237 r_free = 0.3237 target = 0.121180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.097833 restraints weight = 15737.925| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.73 r_work: 0.2825 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13805 Z= 0.253 Angle : 0.616 7.477 18825 Z= 0.307 Chirality : 0.044 0.141 2290 Planarity : 0.004 0.031 2345 Dihedral : 4.237 18.192 1950 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.77 % Allowed : 19.46 % 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: 0.63 (0.21), residues: 1720 helix: 2.26 (0.19), residues: 685 sheet: -0.61 (0.23), residues: 520 loop : -0.91 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 88 HIS 0.005 0.001 HIS A 283 PHE 0.016 0.002 PHE A 251 TYR 0.027 0.002 TYR C 406 ARG 0.003 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 5) link_NAG-ASN : angle 1.07500 ( 15) hydrogen bonds : bond 0.05213 ( 761) hydrogen bonds : angle 4.37689 ( 2382) SS BOND : bond 0.00142 ( 10) SS BOND : angle 1.95609 ( 20) covalent geometry : bond 0.00631 (13790) covalent geometry : angle 0.61242 (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 248 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.501 Fit side-chains REVERT: A 259 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7837 (t80) REVERT: B 259 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7674 (t80) REVERT: B 379 LYS cc_start: 0.7811 (mptt) cc_final: 0.7327 (ttpt) REVERT: C 379 LYS cc_start: 0.7643 (mptt) cc_final: 0.7245 (ttpt) REVERT: D 259 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7687 (t80) REVERT: D 379 LYS cc_start: 0.7802 (mptt) cc_final: 0.7323 (ttpt) REVERT: E 259 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7615 (t80) REVERT: E 263 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7862 (tt) REVERT: E 379 LYS cc_start: 0.7834 (mptt) cc_final: 0.7299 (ttpt) outliers start: 41 outliers final: 30 residues processed: 233 average time/residue: 0.2423 time to fit residues: 83.9189 Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 397 CYS Chi-restraints excluded: chain B residue 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 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 D residue 402 ILE Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 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: 0.7980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.125608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.102596 restraints weight = 15546.773| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.71 r_work: 0.2897 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1892 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= 0.113 Angle : 0.508 8.735 18825 Z= 0.254 Chirality : 0.040 0.136 2290 Planarity : 0.003 0.032 2345 Dihedral : 3.787 14.596 1950 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.89 % Allowed : 20.68 % Favored : 77.43 % 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: 1.01 (0.21), residues: 1720 helix: 2.53 (0.19), residues: 695 sheet: -0.51 (0.23), residues: 525 loop : -0.58 (0.27), residues: 500 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 0.016 0.001 PHE C 384 TYR 0.023 0.001 TYR C 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 0.64896 ( 15) hydrogen bonds : bond 0.04215 ( 761) hydrogen bonds : angle 4.05434 ( 2382) SS BOND : bond 0.00196 ( 10) SS BOND : angle 2.12962 ( 20) covalent geometry : bond 0.00256 (13790) covalent geometry : angle 0.50332 (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 247 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 1.609 Fit side-chains REVERT: A 56 PHE cc_start: 0.7401 (t80) cc_final: 0.6926 (t80) REVERT: A 259 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7625 (t80) REVERT: B 33 MET cc_start: 0.8062 (ttp) cc_final: 0.7654 (ttm) REVERT: B 36 ASP cc_start: 0.7611 (m-30) cc_final: 0.7360 (m-30) REVERT: B 56 PHE cc_start: 0.7431 (t80) cc_final: 0.7141 (t80) REVERT: B 259 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7675 (t80) REVERT: B 379 LYS cc_start: 0.7736 (mptt) cc_final: 0.7344 (ttpt) REVERT: C 259 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7684 (t80) REVERT: C 379 LYS cc_start: 0.7596 (mptt) cc_final: 0.7294 (ttpt) REVERT: D 56 PHE cc_start: 0.7387 (t80) cc_final: 0.7145 (t80) REVERT: D 259 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7696 (t80) REVERT: D 276 CYS cc_start: 0.6856 (m) cc_final: 0.5965 (p) REVERT: D 379 LYS cc_start: 0.7724 (mptt) cc_final: 0.7303 (ttpt) REVERT: E 259 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7641 (t80) REVERT: E 379 LYS cc_start: 0.7783 (mptt) cc_final: 0.7340 (ttpt) outliers start: 28 outliers final: 22 residues processed: 238 average time/residue: 0.2229 time to fit residues: 79.9751 Evaluate side-chains 242 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain B residue 291 LEU 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 263 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 402 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 158 optimal weight: 0.0050 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.124327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.101046 restraints weight = 15611.620| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.75 r_work: 0.2870 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13805 Z= 0.141 Angle : 0.529 8.629 18825 Z= 0.263 Chirality : 0.041 0.136 2290 Planarity : 0.004 0.033 2345 Dihedral : 3.877 15.906 1950 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.89 % Allowed : 20.68 % Favored : 77.43 % 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: 1.00 (0.21), residues: 1720 helix: 2.64 (0.19), residues: 685 sheet: -0.55 (0.23), residues: 525 loop : -0.66 (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 0.001 PHE C 384 TYR 0.023 0.002 TYR C 406 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 5) link_NAG-ASN : angle 0.82381 ( 15) hydrogen bonds : bond 0.04407 ( 761) hydrogen bonds : angle 4.07136 ( 2382) SS BOND : bond 0.00166 ( 10) SS BOND : angle 1.94335 ( 20) covalent geometry : bond 0.00336 (13790) covalent geometry : angle 0.52537 (18790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3440 Ramachandran restraints generated. 1720 Oldfield, 0 Emsley, 1720 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 1.440 Fit side-chains REVERT: A 56 PHE cc_start: 0.7437 (t80) cc_final: 0.6873 (t80) REVERT: A 259 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 33 MET cc_start: 0.8131 (ttp) cc_final: 0.7719 (ttm) REVERT: B 36 ASP cc_start: 0.7650 (m-30) cc_final: 0.7420 (m-30) REVERT: B 56 PHE cc_start: 0.7512 (t80) cc_final: 0.7293 (t80) REVERT: B 259 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7686 (t80) REVERT: B 379 LYS cc_start: 0.7693 (mptt) cc_final: 0.7317 (ttpt) REVERT: C 263 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7952 (tt) REVERT: C 379 LYS cc_start: 0.7577 (mptt) cc_final: 0.7251 (ttpt) REVERT: D 56 PHE cc_start: 0.7462 (t80) cc_final: 0.7144 (t80) REVERT: D 259 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7696 (t80) REVERT: D 379 LYS cc_start: 0.7711 (mptt) cc_final: 0.7301 (ttpt) REVERT: E 259 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7631 (t80) REVERT: E 379 LYS cc_start: 0.7729 (mptt) cc_final: 0.7304 (ttpt) outliers start: 28 outliers final: 22 residues processed: 236 average time/residue: 0.2328 time to fit residues: 82.2863 Evaluate side-chains 243 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain B residue 291 LEU 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 263 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 402 ILE Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain E residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 103 optimal weight: 0.0170 chunk 111 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 164 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN C 267 ASN E 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.126839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.104244 restraints weight = 15590.799| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.70 r_work: 0.2919 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13805 Z= 0.100 Angle : 0.494 9.670 18825 Z= 0.248 Chirality : 0.040 0.130 2290 Planarity : 0.003 0.029 2345 Dihedral : 3.612 13.471 1950 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.09 % Allowed : 20.68 % Favored : 77.23 % 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: 1.28 (0.21), residues: 1720 helix: 2.81 (0.19), residues: 695 sheet: -0.40 (0.24), residues: 525 loop : -0.51 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 81 HIS 0.002 0.001 HIS A 283 PHE 0.017 0.001 PHE C 384 TYR 0.022 0.001 TYR C 406 ARG 0.002 0.000 ARG A 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 5) link_NAG-ASN : angle 0.65526 ( 15) hydrogen bonds : bond 0.03849 ( 761) hydrogen bonds : angle 3.86292 ( 2382) SS BOND : bond 0.00145 ( 10) SS BOND : angle 2.36463 ( 20) covalent geometry : bond 0.00219 (13790) covalent geometry : angle 0.48810 (18790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5759.53 seconds wall clock time: 100 minutes 43.95 seconds (6043.95 seconds total)