Starting phenix.real_space_refine on Thu Mar 5 04:56:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyp_34375/03_2026/8gyp_34375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyp_34375/03_2026/8gyp_34375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gyp_34375/03_2026/8gyp_34375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyp_34375/03_2026/8gyp_34375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gyp_34375/03_2026/8gyp_34375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyp_34375/03_2026/8gyp_34375.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.090 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 98 5.16 5 C 12760 2.51 5 N 3231 2.21 5 O 3449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19538 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2775 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2779 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2770 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2779 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2779 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2779 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2779 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" 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: "G" 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: 4.54, per 1000 atoms: 0.23 Number of scatterers: 19538 At special positions: 0 Unit cell: (127.6, 130.9, 127.6, 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 98 16.00 O 3449 8.00 N 3231 7.00 C 12760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 261 " distance=2.04 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 261 " distance=2.04 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 261 " distance=2.04 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 261 " distance=2.04 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 261 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 261 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 242 " 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 401 " - " ASN A 71 " " NAG B 401 " - " ASN B 71 " " NAG C 401 " - " ASN C 71 " " NAG D 401 " - " ASN D 71 " " NAG E 401 " - " ASN E 71 " " NAG F 401 " - " ASN F 71 " " NAG G 401 " - " ASN G 71 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 884.1 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 7 sheets defined 75.0% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 33 through 61 removed outlier: 4.002A pdb=" N ILE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 157 Proline residue: A 124 - end of helix Proline residue: A 134 - end of helix removed outlier: 3.807A pdb=" N LYS A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.700A pdb=" N PHE A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 265 through 296 Proline residue: A 285 - end of helix removed outlier: 4.398A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 307 removed outlier: 4.150A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.683A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 341 removed outlier: 3.802A pdb=" N VAL A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 32 through 60 removed outlier: 3.946A pdb=" N ARG B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 109 through 133 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 133 through 157 removed outlier: 3.878A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 170 through 183 removed outlier: 3.690A pdb=" N PHE B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 265 through 296 Proline residue: B 285 - end of helix removed outlier: 4.311A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 307 removed outlier: 4.211A pdb=" N MET B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.540A pdb=" N LEU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 341 removed outlier: 3.831A pdb=" N VAL B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 364 through 374 Processing helix chain 'C' and resid 21 through 28 Processing helix chain 'C' and resid 32 through 60 removed outlier: 3.872A pdb=" N ILE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 109 through 157 Proline residue: C 124 - end of helix Proline residue: C 134 - end of helix removed outlier: 3.933A pdb=" N LYS C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 170 through 183 removed outlier: 3.667A pdb=" N PHE C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 265 through 296 Proline residue: C 285 - end of helix removed outlier: 4.454A pdb=" N LEU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N CYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 307 removed outlier: 4.207A pdb=" N MET C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.701A pdb=" N LEU C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 341 removed outlier: 3.690A pdb=" N VAL C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 356 removed outlier: 4.733A pdb=" N LEU C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'D' and resid 21 through 28 Processing helix chain 'D' and resid 33 through 60 removed outlier: 3.879A pdb=" N ILE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 109 through 157 Proline residue: D 124 - end of helix Proline residue: D 134 - end of helix removed outlier: 3.865A pdb=" N LYS D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 170 through 183 removed outlier: 3.760A pdb=" N PHE D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 265 through 296 Proline residue: D 285 - end of helix removed outlier: 4.490A pdb=" N LEU D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 307 removed outlier: 4.211A pdb=" N MET D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.558A pdb=" N LEU D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 341 removed outlier: 3.678A pdb=" N VAL D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 356 Processing helix chain 'D' and resid 364 through 374 Processing helix chain 'E' and resid 21 through 28 Processing helix chain 'E' and resid 33 through 61 removed outlier: 4.172A pdb=" N ILE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 43 " --> pdb=" O LYS E 39 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 109 through 157 Proline residue: E 124 - end of helix Proline residue: E 134 - end of helix removed outlier: 3.848A pdb=" N LYS E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 170 through 183 removed outlier: 3.683A pdb=" N PHE E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 265 through 296 Proline residue: E 285 - end of helix removed outlier: 4.293A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N CYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 307 removed outlier: 4.340A pdb=" N MET E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 removed outlier: 4.583A pdb=" N LEU E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 341 removed outlier: 3.886A pdb=" N VAL E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 356 Processing helix chain 'E' and resid 364 through 374 Processing helix chain 'F' and resid 21 through 28 Processing helix chain 'F' and resid 33 through 61 removed outlier: 4.126A pdb=" N ILE F 37 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 109 through 157 Proline residue: F 124 - end of helix Proline residue: F 134 - end of helix removed outlier: 3.836A pdb=" N LYS F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 168 Processing helix chain 'F' and resid 170 through 183 removed outlier: 3.680A pdb=" N PHE F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 203 through 230 Processing helix chain 'F' and resid 265 through 296 Proline residue: F 285 - end of helix removed outlier: 4.542A pdb=" N LEU F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N CYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG F 296 " --> pdb=" O THR F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 307 removed outlier: 4.163A pdb=" N MET F 307 " --> pdb=" O SER F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 316 removed outlier: 3.866A pdb=" N LEU F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 341 removed outlier: 3.830A pdb=" N VAL F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE F 341 " --> pdb=" O ILE F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 356 Processing helix chain 'F' and resid 364 through 374 Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'G' and resid 33 through 61 removed outlier: 4.131A pdb=" N ILE G 37 " --> pdb=" O PRO G 33 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 109 through 157 Proline residue: G 124 - end of helix Proline residue: G 134 - end of helix removed outlier: 3.785A pdb=" N LYS G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 168 Processing helix chain 'G' and resid 170 through 183 removed outlier: 3.705A pdb=" N PHE G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 203 through 230 Processing helix chain 'G' and resid 265 through 295 Proline residue: G 285 - end of helix removed outlier: 4.426A pdb=" N LEU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 307 removed outlier: 4.216A pdb=" N MET G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 316 removed outlier: 3.550A pdb=" N LEU G 313 " --> pdb=" O PRO G 309 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 341 removed outlier: 3.839A pdb=" N VAL G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE G 341 " --> pdb=" O ILE G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 356 Processing helix chain 'G' and resid 364 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1265 hydrogen bonds defined for protein. 3753 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: 3.08 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6020 1.35 - 1.47: 5104 1.47 - 1.60: 8729 1.60 - 1.72: 0 1.72 - 1.85: 140 Bond restraints: 19993 Sorted by residual: bond pdb=" C5 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" C5 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CB CYS D 66 " pdb=" SG CYS D 66 " ideal model delta sigma weight residual 1.808 1.845 -0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" C5 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 19988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 26554 1.68 - 3.35: 452 3.35 - 5.03: 117 5.03 - 6.71: 12 6.71 - 8.39: 9 Bond angle restraints: 27144 Sorted by residual: angle pdb=" CA CYS C 261 " pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " ideal model delta sigma weight residual 114.40 121.95 -7.55 2.30e+00 1.89e-01 1.08e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.42 109.66 3.76 1.17e+00 7.31e-01 1.03e+01 angle pdb=" CA CYS F 261 " pdb=" CB CYS F 261 " pdb=" SG CYS F 261 " ideal model delta sigma weight residual 114.40 121.70 -7.30 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS E 261 " pdb=" CB CYS E 261 " pdb=" SG CYS E 261 " ideal model delta sigma weight residual 114.40 121.66 -7.26 2.30e+00 1.89e-01 9.95e+00 angle pdb=" CA CYS B 261 " pdb=" CB CYS B 261 " pdb=" SG CYS B 261 " ideal model delta sigma weight residual 114.40 121.64 -7.24 2.30e+00 1.89e-01 9.92e+00 ... (remaining 27139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10297 17.76 - 35.51: 1364 35.51 - 53.27: 422 53.27 - 71.02: 53 71.02 - 88.78: 20 Dihedral angle restraints: 12156 sinusoidal: 4869 harmonic: 7287 Sorted by residual: dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 261 " pdb=" CB CYS C 261 " ideal model delta sinusoidal sigma weight residual 93.00 39.58 53.42 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" CB CYS E 66 " pdb=" SG CYS E 66 " pdb=" SG CYS E 261 " pdb=" CB CYS E 261 " ideal model delta sinusoidal sigma weight residual 93.00 39.69 53.31 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual 93.00 39.80 53.20 1 1.00e+01 1.00e-02 3.85e+01 ... (remaining 12153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 2025 0.023 - 0.047: 665 0.047 - 0.070: 264 0.070 - 0.093: 187 0.093 - 0.116: 64 Chirality restraints: 3205 Sorted by residual: chirality pdb=" CA ILE D 259 " pdb=" N ILE D 259 " pdb=" C ILE D 259 " pdb=" CB ILE D 259 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA PRO G 124 " pdb=" N PRO G 124 " pdb=" C PRO G 124 " pdb=" CB PRO G 124 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.08e-01 chirality pdb=" CA PRO A 124 " pdb=" N PRO A 124 " pdb=" C PRO A 124 " pdb=" CB PRO A 124 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.07e-01 ... (remaining 3202 not shown) Planarity restraints: 3323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 71 " -0.096 2.00e-02 2.50e+03 2.15e-01 5.78e+02 pdb=" CG ASN E 71 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN E 71 " -0.112 2.00e-02 2.50e+03 pdb=" ND2 ASN E 71 " 0.387 2.00e-02 2.50e+03 pdb=" C1 NAG E 401 " -0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 71 " -0.087 2.00e-02 2.50e+03 1.84e-01 4.22e+02 pdb=" CG ASN C 71 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN C 71 " -0.092 2.00e-02 2.50e+03 pdb=" ND2 ASN C 71 " 0.330 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 71 " 0.091 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" CG ASN A 71 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 71 " 0.087 2.00e-02 2.50e+03 pdb=" ND2 ASN A 71 " -0.330 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.202 2.00e-02 2.50e+03 ... (remaining 3320 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 250 2.61 - 3.18: 18387 3.18 - 3.76: 29903 3.76 - 4.33: 37865 4.33 - 4.90: 63703 Nonbonded interactions: 150108 Sorted by model distance: nonbonded pdb=" OD1 ASP E 139 " pdb=" OH TYR E 195 " model vdw 2.040 3.040 nonbonded pdb=" OH TYR A 224 " pdb=" OG1 THR A 281 " model vdw 2.077 3.040 nonbonded pdb=" O ILE G 323 " pdb=" ND2 ASN G 324 " model vdw 2.136 3.120 nonbonded pdb=" O ILE C 323 " pdb=" ND2 ASN C 324 " model vdw 2.146 3.120 nonbonded pdb=" OE1 GLN A 98 " pdb=" NZ LYS A 102 " model vdw 2.168 3.120 ... (remaining 150103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 152 or (resid 153 and (name N or name CA or nam \ e C or name O or name CB )) or resid 154 or (resid 155 and (name N or name CA or \ name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'B' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'C' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 401)) selection = (chain 'D' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'E' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'F' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'G' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.170 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20014 Z= 0.149 Angle : 0.740 33.717 27193 Z= 0.338 Chirality : 0.034 0.116 3205 Planarity : 0.004 0.047 3316 Dihedral : 17.319 88.775 7354 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.23 % Favored : 92.44 % Rotamer: Outliers : 0.09 % Allowed : 27.96 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2408 helix: 1.29 (0.13), residues: 1701 sheet: None (None), residues: 0 loop : -1.59 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 316 TYR 0.014 0.001 TYR G 130 PHE 0.010 0.001 PHE E 142 TRP 0.014 0.001 TRP A 345 HIS 0.002 0.000 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00288 (19993) covalent geometry : angle 0.58879 (27144) SS BOND : bond 0.00464 ( 14) SS BOND : angle 2.24792 ( 28) hydrogen bonds : bond 0.13180 ( 1265) hydrogen bonds : angle 5.74588 ( 3753) link_NAG-ASN : bond 0.06387 ( 7) link_NAG-ASN : angle 15.95384 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 GLN cc_start: 0.5762 (mp10) cc_final: 0.5464 (mp10) REVERT: C 122 TYR cc_start: 0.7999 (t80) cc_final: 0.7704 (t80) REVERT: C 163 LYS cc_start: 0.7682 (mmmt) cc_final: 0.7207 (mttm) REVERT: D 195 TYR cc_start: 0.7790 (t80) cc_final: 0.7589 (t80) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.1320 time to fit residues: 47.6003 Evaluate side-chains 210 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN C 324 ASN E 324 ASN G 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.207182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.176204 restraints weight = 22452.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175276 restraints weight = 43040.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.175574 restraints weight = 38050.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174927 restraints weight = 26131.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.175363 restraints weight = 24649.294| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20014 Z= 0.172 Angle : 0.767 11.593 27193 Z= 0.357 Chirality : 0.040 0.249 3205 Planarity : 0.004 0.039 3316 Dihedral : 6.734 58.266 2799 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.36 % Favored : 94.31 % Rotamer: Outliers : 4.18 % Allowed : 24.20 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2408 helix: 1.66 (0.13), residues: 1694 sheet: -3.47 (0.49), residues: 70 loop : -1.63 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 165 TYR 0.012 0.001 TYR A 280 PHE 0.017 0.002 PHE G 269 TRP 0.010 0.001 TRP A 345 HIS 0.003 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00403 (19993) covalent geometry : angle 0.74300 (27144) SS BOND : bond 0.00854 ( 14) SS BOND : angle 2.10627 ( 28) hydrogen bonds : bond 0.04741 ( 1265) hydrogen bonds : angle 4.03751 ( 3753) link_NAG-ASN : bond 0.00459 ( 7) link_NAG-ASN : angle 6.49963 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 245 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7510 (t) REVERT: C 133 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7576 (t) REVERT: C 318 MET cc_start: 0.7597 (mmm) cc_final: 0.7268 (mmp) REVERT: E 101 MET cc_start: 0.4015 (tpp) cc_final: 0.3786 (tpp) REVERT: E 192 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7429 (mp) REVERT: F 47 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8310 (mp) outliers start: 90 outliers final: 54 residues processed: 314 average time/residue: 0.1083 time to fit residues: 56.1245 Evaluate side-chains 282 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 295 CYS Chi-restraints excluded: chain G residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 185 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.206467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.175838 restraints weight = 22762.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.174818 restraints weight = 43687.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.174566 restraints weight = 37940.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173037 restraints weight = 31270.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173693 restraints weight = 26475.692| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20014 Z= 0.161 Angle : 0.734 10.176 27193 Z= 0.343 Chirality : 0.039 0.264 3205 Planarity : 0.004 0.060 3316 Dihedral : 5.666 45.782 2799 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.15 % Favored : 94.52 % Rotamer: Outliers : 4.92 % Allowed : 24.48 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.18), residues: 2408 helix: 1.85 (0.12), residues: 1701 sheet: -3.39 (0.44), residues: 70 loop : -1.46 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 201 TYR 0.013 0.001 TYR A 280 PHE 0.016 0.001 PHE E 269 TRP 0.009 0.001 TRP A 345 HIS 0.002 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00373 (19993) covalent geometry : angle 0.70862 (27144) SS BOND : bond 0.00884 ( 14) SS BOND : angle 2.17301 ( 28) hydrogen bonds : bond 0.04463 ( 1265) hydrogen bonds : angle 3.89542 ( 3753) link_NAG-ASN : bond 0.00673 ( 7) link_NAG-ASN : angle 6.47250 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 242 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7893 (mt) REVERT: A 323 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7997 (tp) REVERT: B 263 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7987 (pt) REVERT: C 101 MET cc_start: 0.4002 (ppp) cc_final: 0.3535 (ppp) REVERT: E 192 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7440 (mp) REVERT: F 263 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8029 (pt) REVERT: G 263 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7867 (pt) outliers start: 106 outliers final: 77 residues processed: 327 average time/residue: 0.1076 time to fit residues: 58.1705 Evaluate side-chains 311 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 228 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 31 optimal weight: 3.9990 chunk 223 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 chunk 43 optimal weight: 0.0870 chunk 244 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS E 213 ASN ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.229664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181276 restraints weight = 24384.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178209 restraints weight = 40515.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181445 restraints weight = 31336.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.181047 restraints weight = 19273.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.181684 restraints weight = 19051.192| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20014 Z= 0.142 Angle : 0.699 10.330 27193 Z= 0.328 Chirality : 0.038 0.240 3205 Planarity : 0.004 0.049 3316 Dihedral : 4.962 34.518 2799 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.77 % Favored : 93.90 % Rotamer: Outliers : 4.97 % Allowed : 25.41 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.18), residues: 2408 helix: 1.99 (0.12), residues: 1694 sheet: -3.38 (0.43), residues: 70 loop : -1.47 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 201 TYR 0.011 0.001 TYR B 289 PHE 0.016 0.001 PHE E 269 TRP 0.009 0.001 TRP A 345 HIS 0.002 0.000 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00321 (19993) covalent geometry : angle 0.67486 (27144) SS BOND : bond 0.00879 ( 14) SS BOND : angle 2.03964 ( 28) hydrogen bonds : bond 0.04120 ( 1265) hydrogen bonds : angle 3.73654 ( 3753) link_NAG-ASN : bond 0.00633 ( 7) link_NAG-ASN : angle 6.16679 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 257 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8031 (tp) REVERT: C 101 MET cc_start: 0.4382 (ppp) cc_final: 0.3870 (ppp) REVERT: C 122 TYR cc_start: 0.8018 (t80) cc_final: 0.7795 (t80) REVERT: E 192 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7168 (mp) outliers start: 107 outliers final: 72 residues processed: 339 average time/residue: 0.1102 time to fit residues: 61.0993 Evaluate side-chains 312 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 238 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 181 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 233 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 148 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS B 213 ASN E 159 GLN E 213 ASN E 254 HIS ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.231207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.184321 restraints weight = 24270.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.181215 restraints weight = 39668.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.183952 restraints weight = 32663.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.184034 restraints weight = 19751.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.185092 restraints weight = 19041.053| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20014 Z= 0.137 Angle : 0.695 10.432 27193 Z= 0.326 Chirality : 0.038 0.243 3205 Planarity : 0.004 0.039 3316 Dihedral : 4.610 25.588 2799 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.65 % Favored : 94.02 % Rotamer: Outliers : 5.48 % Allowed : 25.17 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2408 helix: 2.04 (0.13), residues: 1694 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.010 0.001 TYR E 195 PHE 0.015 0.001 PHE C 269 TRP 0.009 0.001 TRP A 345 HIS 0.002 0.000 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00309 (19993) covalent geometry : angle 0.67365 (27144) SS BOND : bond 0.00872 ( 14) SS BOND : angle 1.98502 ( 28) hydrogen bonds : bond 0.03974 ( 1265) hydrogen bonds : angle 3.67695 ( 3753) link_NAG-ASN : bond 0.00576 ( 7) link_NAG-ASN : angle 5.77177 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 257 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7552 (pt) REVERT: A 323 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8021 (tp) REVERT: B 263 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7950 (pt) REVERT: C 101 MET cc_start: 0.4291 (ppp) cc_final: 0.3777 (ppp) REVERT: C 122 TYR cc_start: 0.8036 (t80) cc_final: 0.7770 (t80) REVERT: C 307 MET cc_start: 0.7228 (ttt) cc_final: 0.6981 (tpt) REVERT: D 128 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.7579 (t-100) REVERT: E 31 GLU cc_start: 0.7777 (pm20) cc_final: 0.7295 (tp30) REVERT: E 101 MET cc_start: 0.3925 (tpp) cc_final: 0.3653 (tpp) REVERT: E 263 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7642 (pt) REVERT: G 263 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7784 (pt) outliers start: 118 outliers final: 87 residues processed: 344 average time/residue: 0.1101 time to fit residues: 62.1065 Evaluate side-chains 339 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 246 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 128 TRP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 5 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 148 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN E 254 HIS ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.229907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.184602 restraints weight = 24180.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.181721 restraints weight = 41589.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.183941 restraints weight = 35900.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.184317 restraints weight = 21910.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.184966 restraints weight = 20853.095| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20014 Z= 0.139 Angle : 0.690 10.582 27193 Z= 0.323 Chirality : 0.038 0.226 3205 Planarity : 0.004 0.040 3316 Dihedral : 4.397 21.215 2799 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.86 % Favored : 93.81 % Rotamer: Outliers : 6.08 % Allowed : 24.62 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.18), residues: 2408 helix: 2.05 (0.12), residues: 1694 sheet: -3.29 (0.44), residues: 70 loop : -1.37 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.010 0.001 TYR A 280 PHE 0.015 0.001 PHE E 269 TRP 0.009 0.001 TRP A 345 HIS 0.004 0.001 HIS E 160 Details of bonding type rmsd covalent geometry : bond 0.00316 (19993) covalent geometry : angle 0.67024 (27144) SS BOND : bond 0.00852 ( 14) SS BOND : angle 2.02543 ( 28) hydrogen bonds : bond 0.03938 ( 1265) hydrogen bonds : angle 3.65717 ( 3753) link_NAG-ASN : bond 0.00565 ( 7) link_NAG-ASN : angle 5.47976 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 260 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7946 (tt) REVERT: A 323 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8023 (tp) REVERT: B 128 TRP cc_start: 0.8100 (OUTLIER) cc_final: 0.7887 (t-100) REVERT: B 263 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7977 (pt) REVERT: C 101 MET cc_start: 0.4288 (ppp) cc_final: 0.3800 (ppp) REVERT: C 122 TYR cc_start: 0.8050 (t80) cc_final: 0.7790 (t80) REVERT: C 263 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7709 (pt) REVERT: D 126 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7849 (tt) REVERT: D 128 TRP cc_start: 0.8054 (OUTLIER) cc_final: 0.7558 (t-100) REVERT: D 337 ILE cc_start: 0.8165 (tt) cc_final: 0.7875 (pt) REVERT: E 31 GLU cc_start: 0.7672 (pm20) cc_final: 0.7321 (tp30) REVERT: E 101 MET cc_start: 0.4281 (tpp) cc_final: 0.3949 (tpp) REVERT: E 192 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7193 (mp) REVERT: E 263 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7734 (pt) REVERT: E 276 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7938 (m) REVERT: F 263 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7961 (pt) REVERT: G 263 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7801 (pt) REVERT: G 283 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.6860 (mp) outliers start: 131 outliers final: 96 residues processed: 364 average time/residue: 0.1075 time to fit residues: 64.4548 Evaluate side-chains 360 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 251 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 343 PHE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 TRP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 128 TRP Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 189 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 128 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 193 optimal weight: 0.0970 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.232647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.185558 restraints weight = 24364.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.182130 restraints weight = 40308.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.185313 restraints weight = 32812.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.184777 restraints weight = 20360.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.185876 restraints weight = 19795.726| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20014 Z= 0.128 Angle : 0.685 9.935 27193 Z= 0.319 Chirality : 0.037 0.212 3205 Planarity : 0.004 0.040 3316 Dihedral : 4.229 23.424 2799 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.32 % Favored : 94.35 % Rotamer: Outliers : 4.64 % Allowed : 26.61 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.18), residues: 2408 helix: 2.13 (0.12), residues: 1694 sheet: None (None), residues: 0 loop : -1.58 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 182 TYR 0.017 0.001 TYR F 186 PHE 0.014 0.001 PHE B 269 TRP 0.009 0.001 TRP A 345 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00283 (19993) covalent geometry : angle 0.66870 (27144) SS BOND : bond 0.00848 ( 14) SS BOND : angle 1.90192 ( 28) hydrogen bonds : bond 0.03717 ( 1265) hydrogen bonds : angle 3.58538 ( 3753) link_NAG-ASN : bond 0.00436 ( 7) link_NAG-ASN : angle 4.96065 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 262 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8037 (tp) REVERT: B 128 TRP cc_start: 0.8006 (OUTLIER) cc_final: 0.7677 (t-100) REVERT: C 101 MET cc_start: 0.4010 (ppp) cc_final: 0.3654 (ppp) REVERT: D 128 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.7326 (t-100) REVERT: D 337 ILE cc_start: 0.8122 (tt) cc_final: 0.7827 (pt) REVERT: E 31 GLU cc_start: 0.7661 (pm20) cc_final: 0.7106 (tp30) REVERT: E 101 MET cc_start: 0.3986 (tpp) cc_final: 0.3661 (tpp) REVERT: E 276 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7728 (m) REVERT: E 283 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6690 (mp) REVERT: G 248 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6518 (pp) REVERT: G 283 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.6851 (mp) outliers start: 100 outliers final: 77 residues processed: 337 average time/residue: 0.1113 time to fit residues: 62.0242 Evaluate side-chains 337 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 253 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 295 CYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 128 TRP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 128 TRP Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 218 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS B 237 GLN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN E 254 HIS ** G 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.226107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.178302 restraints weight = 24386.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.175649 restraints weight = 39280.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.178027 restraints weight = 35984.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.178312 restraints weight = 19511.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179130 restraints weight = 18340.726| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20014 Z= 0.204 Angle : 0.772 11.043 27193 Z= 0.363 Chirality : 0.041 0.203 3205 Planarity : 0.004 0.041 3316 Dihedral : 4.384 20.510 2799 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.61 % Favored : 94.06 % Rotamer: Outliers : 5.53 % Allowed : 26.38 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.18), residues: 2408 helix: 1.85 (0.12), residues: 1708 sheet: -2.99 (0.45), residues: 70 loop : -1.34 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.015 0.002 TYR A 280 PHE 0.017 0.002 PHE B 269 TRP 0.012 0.001 TRP B 85 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00491 (19993) covalent geometry : angle 0.75048 (27144) SS BOND : bond 0.00881 ( 14) SS BOND : angle 2.59792 ( 28) hydrogen bonds : bond 0.04693 ( 1265) hydrogen bonds : angle 3.87171 ( 3753) link_NAG-ASN : bond 0.00853 ( 7) link_NAG-ASN : angle 5.85692 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 260 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.7628 (ttm) cc_final: 0.7366 (tmm) REVERT: A 126 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7875 (tt) REVERT: A 263 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7922 (pt) REVERT: A 323 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8191 (tp) REVERT: B 263 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8219 (pt) REVERT: C 101 MET cc_start: 0.4695 (ppp) cc_final: 0.4157 (ppp) REVERT: C 263 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8021 (pt) REVERT: D 126 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7800 (tp) REVERT: D 128 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7755 (t-100) REVERT: E 31 GLU cc_start: 0.7622 (pm20) cc_final: 0.7181 (tp30) REVERT: E 263 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8003 (pt) REVERT: E 283 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7558 (mt) REVERT: F 263 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8247 (pt) REVERT: G 283 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7701 (mt) outliers start: 119 outliers final: 95 residues processed: 359 average time/residue: 0.1105 time to fit residues: 65.4026 Evaluate side-chains 344 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 238 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 345 TRP Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 TRP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 133 optimal weight: 7.9990 chunk 113 optimal weight: 0.0870 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 0.0000 chunk 105 optimal weight: 40.0000 chunk 179 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 101 optimal weight: 0.0970 chunk 152 optimal weight: 0.9980 overall best weight: 0.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 HIS B 254 HIS ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.232760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.185099 restraints weight = 24224.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.182463 restraints weight = 37298.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.184646 restraints weight = 31081.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.185087 restraints weight = 19922.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.185263 restraints weight = 19152.858| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20014 Z= 0.132 Angle : 0.712 11.531 27193 Z= 0.332 Chirality : 0.038 0.206 3205 Planarity : 0.004 0.040 3316 Dihedral : 4.202 25.859 2799 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.40 % Favored : 94.27 % Rotamer: Outliers : 3.86 % Allowed : 27.78 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.18), residues: 2408 helix: 2.08 (0.12), residues: 1694 sheet: None (None), residues: 0 loop : -1.60 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 182 TYR 0.016 0.001 TYR E 130 PHE 0.014 0.001 PHE F 187 TRP 0.010 0.001 TRP A 345 HIS 0.002 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00289 (19993) covalent geometry : angle 0.69779 (27144) SS BOND : bond 0.00876 ( 14) SS BOND : angle 1.99109 ( 28) hydrogen bonds : bond 0.03717 ( 1265) hydrogen bonds : angle 3.60480 ( 3753) link_NAG-ASN : bond 0.00327 ( 7) link_NAG-ASN : angle 4.65914 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 258 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8059 (tp) REVERT: B 101 MET cc_start: 0.3676 (tpp) cc_final: 0.3254 (tpp) REVERT: B 128 TRP cc_start: 0.7957 (OUTLIER) cc_final: 0.7603 (t-100) REVERT: C 101 MET cc_start: 0.4274 (ppp) cc_final: 0.3926 (ppp) REVERT: D 128 TRP cc_start: 0.7987 (OUTLIER) cc_final: 0.7410 (t-100) REVERT: D 283 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6800 (mp) REVERT: G 283 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.6822 (mp) outliers start: 83 outliers final: 64 residues processed: 316 average time/residue: 0.1172 time to fit residues: 61.2449 Evaluate side-chains 316 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 247 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 128 TRP Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 128 TRP Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 221 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.222636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179067 restraints weight = 23269.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.177043 restraints weight = 41293.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.179569 restraints weight = 30988.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.179288 restraints weight = 21025.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.179718 restraints weight = 19489.056| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20014 Z= 0.149 Angle : 0.738 11.803 27193 Z= 0.342 Chirality : 0.039 0.232 3205 Planarity : 0.004 0.041 3316 Dihedral : 4.128 26.439 2799 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 3.44 % Allowed : 28.75 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2408 helix: 2.08 (0.12), residues: 1694 sheet: -3.14 (0.45), residues: 70 loop : -1.40 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.015 0.001 TYR G 122 PHE 0.016 0.001 PHE E 269 TRP 0.008 0.001 TRP A 345 HIS 0.002 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00350 (19993) covalent geometry : angle 0.72276 (27144) SS BOND : bond 0.00854 ( 14) SS BOND : angle 2.21585 ( 28) hydrogen bonds : bond 0.03991 ( 1265) hydrogen bonds : angle 3.65849 ( 3753) link_NAG-ASN : bond 0.00552 ( 7) link_NAG-ASN : angle 4.82004 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 247 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 MET cc_start: 0.7488 (mmm) cc_final: 0.7232 (mmp) REVERT: A 323 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (tp) REVERT: B 101 MET cc_start: 0.4015 (tpp) cc_final: 0.3555 (tpp) REVERT: B 128 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.7718 (t-100) REVERT: C 101 MET cc_start: 0.4443 (ppp) cc_final: 0.4073 (ppp) REVERT: D 128 TRP cc_start: 0.8133 (OUTLIER) cc_final: 0.7543 (t-100) REVERT: D 283 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7404 (mt) outliers start: 74 outliers final: 68 residues processed: 302 average time/residue: 0.1153 time to fit residues: 57.1625 Evaluate side-chains 308 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 128 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 252 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 128 TRP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 342 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 187 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 337 ILE Chi-restraints excluded: chain F residue 340 LEU Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 128 TRP Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 345 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 243 optimal weight: 0.3980 chunk 242 optimal weight: 1.9990 chunk 233 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.232371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.185308 restraints weight = 24466.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.182815 restraints weight = 37677.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.184879 restraints weight = 31066.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.185285 restraints weight = 19865.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.185518 restraints weight = 19797.890| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20014 Z= 0.131 Angle : 0.714 11.762 27193 Z= 0.329 Chirality : 0.038 0.235 3205 Planarity : 0.004 0.040 3316 Dihedral : 4.079 28.492 2799 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.48 % Favored : 94.23 % Rotamer: Outliers : 3.62 % Allowed : 28.33 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2408 helix: 2.14 (0.12), residues: 1694 sheet: -3.41 (0.43), residues: 70 loop : -1.35 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 201 TYR 0.015 0.001 TYR G 130 PHE 0.014 0.001 PHE B 269 TRP 0.009 0.001 TRP A 345 HIS 0.002 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00295 (19993) covalent geometry : angle 0.70151 (27144) SS BOND : bond 0.00837 ( 14) SS BOND : angle 1.97729 ( 28) hydrogen bonds : bond 0.03653 ( 1265) hydrogen bonds : angle 3.56971 ( 3753) link_NAG-ASN : bond 0.00339 ( 7) link_NAG-ASN : angle 4.24914 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.45 seconds wall clock time: 46 minutes 50.30 seconds (2810.30 seconds total)