Starting phenix.real_space_refine on Tue Jun 17 01:46:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyp_34375/06_2025/8gyp_34375.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyp_34375/06_2025/8gyp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyp_34375/06_2025/8gyp_34375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyp_34375/06_2025/8gyp_34375.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyp_34375/06_2025/8gyp_34375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyp_34375/06_2025/8gyp_34375.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: 11.74, per 1000 atoms: 0.60 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: 4.97 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.96 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: 6.06 Time building geometry restraints manager: 5.90 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 374 or resid 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 374 or resi \ d 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 374 or resid 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 374 or resi \ d 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 374 or resi \ d 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 374 or resi \ d 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 374 or resi \ d 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.750 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.330 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 TRP 0.014 0.001 TRP A 345 HIS 0.002 0.000 HIS E 231 PHE 0.010 0.001 PHE E 142 TYR 0.014 0.001 TYR G 130 ARG 0.002 0.000 ARG G 316 Details of bonding type rmsd link_NAG-ASN : bond 0.06387 ( 7) link_NAG-ASN : angle 15.95384 ( 21) hydrogen bonds : bond 0.13180 ( 1265) hydrogen bonds : angle 5.74588 ( 3753) SS BOND : bond 0.00464 ( 14) SS BOND : angle 2.24792 ( 28) covalent geometry : bond 0.00288 (19993) covalent geometry : angle 0.58879 (27144) *********************** 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 : 2.139 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: 0.3012 time to fit residues: 107.6596 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 : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 74 optimal weight: 0.0570 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.208376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175774 restraints weight = 22577.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.174541 restraints weight = 44084.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175397 restraints weight = 36799.134| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20014 Z= 0.159 Angle : 0.749 11.372 27193 Z= 0.348 Chirality : 0.039 0.254 3205 Planarity : 0.004 0.039 3316 Dihedral : 6.745 58.825 2799 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.15 % Favored : 94.52 % Rotamer: Outliers : 3.58 % Allowed : 24.43 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2408 helix: 1.76 (0.13), residues: 1694 sheet: None (None), residues: 0 loop : -1.83 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 345 HIS 0.004 0.001 HIS B 107 PHE 0.015 0.001 PHE G 269 TYR 0.010 0.001 TYR A 280 ARG 0.004 0.000 ARG E 165 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 7) link_NAG-ASN : angle 6.20510 ( 21) hydrogen bonds : bond 0.04630 ( 1265) hydrogen bonds : angle 3.97702 ( 3753) SS BOND : bond 0.00853 ( 14) SS BOND : angle 1.90363 ( 28) covalent geometry : bond 0.00359 (19993) covalent geometry : angle 0.72659 (27144) *********************** 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 324 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 247 time to evaluate : 2.052 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: C 133 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7579 (t) REVERT: C 318 MET cc_start: 0.7331 (mmm) cc_final: 0.7025 (mmp) REVERT: E 101 MET cc_start: 0.3927 (tpp) cc_final: 0.3631 (tpp) REVERT: E 192 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7480 (mp) REVERT: F 47 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8233 (mp) outliers start: 77 outliers final: 44 residues processed: 307 average time/residue: 0.2648 time to fit residues: 131.6521 Evaluate side-chains 273 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 260 THR 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 340 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 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 202 SER Chi-restraints excluded: chain D residue 232 LEU 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 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 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 337 ILE Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 232 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 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 51 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 224 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.205175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172827 restraints weight = 22668.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171202 restraints weight = 45673.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.171570 restraints weight = 40154.369| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20014 Z= 0.176 Angle : 0.751 10.032 27193 Z= 0.352 Chirality : 0.040 0.261 3205 Planarity : 0.004 0.065 3316 Dihedral : 5.698 47.412 2799 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.48 % Favored : 94.19 % Rotamer: Outliers : 5.06 % Allowed : 24.43 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2408 helix: 1.81 (0.12), residues: 1701 sheet: -3.42 (0.43), residues: 70 loop : -1.48 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 85 HIS 0.003 0.001 HIS B 254 PHE 0.016 0.002 PHE E 269 TYR 0.014 0.001 TYR A 280 ARG 0.004 0.000 ARG F 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 7) link_NAG-ASN : angle 6.53957 ( 21) hydrogen bonds : bond 0.04621 ( 1265) hydrogen bonds : angle 3.94024 ( 3753) SS BOND : bond 0.00887 ( 14) SS BOND : angle 2.27855 ( 28) covalent geometry : bond 0.00415 (19993) covalent geometry : angle 0.72615 (27144) *********************** 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 355 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 246 time to evaluate : 1.992 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: 0.8200 (OUTLIER) cc_final: 0.7937 (tt) REVERT: A 323 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7950 (tp) REVERT: B 263 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8041 (pt) REVERT: C 101 MET cc_start: 0.4184 (ppp) cc_final: 0.3715 (ppp) REVERT: C 263 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7984 (pt) REVERT: E 192 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7511 (mp) REVERT: F 263 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8088 (pt) REVERT: G 263 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7996 (pt) outliers start: 109 outliers final: 78 residues processed: 332 average time/residue: 0.2647 time to fit residues: 142.8869 Evaluate side-chains 308 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 223 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 73 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 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 340 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 343 PHE 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 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 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 232 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 F residue 32 LEU 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 G residue 40 PHE Chi-restraints excluded: chain G residue 50 MET 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 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 44 optimal weight: 0.8980 chunk 35 optimal weight: 40.0000 chunk 129 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN B 213 ASN ** C 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4667 r_free = 0.4667 target = 0.222045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.183637 restraints weight = 23372.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.182319 restraints weight = 37759.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.183715 restraints weight = 35099.782| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20014 Z= 0.152 Angle : 0.710 10.264 27193 Z= 0.334 Chirality : 0.039 0.245 3205 Planarity : 0.004 0.042 3316 Dihedral : 5.063 37.576 2799 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.61 % Favored : 94.06 % Rotamer: Outliers : 5.48 % Allowed : 25.08 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.18), residues: 2408 helix: 1.92 (0.12), residues: 1701 sheet: -3.32 (0.44), residues: 70 loop : -1.42 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 345 HIS 0.002 0.000 HIS F 254 PHE 0.016 0.001 PHE F 269 TYR 0.011 0.001 TYR A 280 ARG 0.003 0.000 ARG F 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 7) link_NAG-ASN : angle 6.30080 ( 21) hydrogen bonds : bond 0.04274 ( 1265) hydrogen bonds : angle 3.79302 ( 3753) SS BOND : bond 0.00883 ( 14) SS BOND : angle 2.14060 ( 28) covalent geometry : bond 0.00348 (19993) covalent geometry : angle 0.68563 (27144) *********************** 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 371 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 253 time to evaluate : 2.282 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 263 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7717 (pt) REVERT: A 323 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8105 (tp) REVERT: C 101 MET cc_start: 0.4275 (ppp) cc_final: 0.3777 (ppp) REVERT: C 122 TYR cc_start: 0.8029 (t80) cc_final: 0.7814 (t80) REVERT: E 31 GLU cc_start: 0.7845 (pm20) cc_final: 0.7490 (tp30) REVERT: E 263 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7700 (pt) REVERT: F 47 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8317 (mp) REVERT: F 122 TYR cc_start: 0.8043 (t80) cc_final: 0.7831 (t80) outliers start: 118 outliers final: 82 residues processed: 346 average time/residue: 0.2758 time to fit residues: 152.8339 Evaluate side-chains 327 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 241 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 255 VAL 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 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 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 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 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 40 PHE Chi-restraints excluded: chain D residue 133 VAL 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 295 CYS 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 191 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 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 47 LEU 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 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 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 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 101 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 91 optimal weight: 0.0470 chunk 94 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS C 254 HIS ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS ** 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 = 0.4713 r_free = 0.4713 target = 0.232256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.184841 restraints weight = 24387.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.182363 restraints weight = 38690.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.185321 restraints weight = 30914.527| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2391 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= 0.131 Angle : 0.686 10.269 27193 Z= 0.320 Chirality : 0.037 0.224 3205 Planarity : 0.004 0.039 3316 Dihedral : 4.583 25.107 2799 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.69 % Favored : 93.98 % Rotamer: Outliers : 4.55 % Allowed : 26.34 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2408 helix: 2.07 (0.13), residues: 1694 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 345 HIS 0.002 0.000 HIS B 107 PHE 0.015 0.001 PHE B 269 TYR 0.009 0.001 TYR A 280 ARG 0.005 0.000 ARG A 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 7) link_NAG-ASN : angle 5.63156 ( 21) hydrogen bonds : bond 0.03842 ( 1265) hydrogen bonds : angle 3.63577 ( 3753) SS BOND : bond 0.00879 ( 14) SS BOND : angle 1.90097 ( 28) covalent geometry : bond 0.00288 (19993) covalent geometry : angle 0.66605 (27144) *********************** 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 362 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 264 time to evaluate : 2.154 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: 0.8349 (OUTLIER) cc_final: 0.8021 (tp) REVERT: C 101 MET cc_start: 0.4265 (ppp) cc_final: 0.3760 (ppp) REVERT: C 122 TYR cc_start: 0.8040 (t80) cc_final: 0.7767 (t80) REVERT: C 307 MET cc_start: 0.7226 (ttt) cc_final: 0.6981 (tpt) REVERT: D 128 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.7576 (t-100) REVERT: D 337 ILE cc_start: 0.8153 (tt) cc_final: 0.7840 (pt) REVERT: E 31 GLU cc_start: 0.7785 (pm20) cc_final: 0.7379 (tp30) REVERT: E 101 MET cc_start: 0.3903 (tpp) cc_final: 0.3567 (tpp) outliers start: 98 outliers final: 73 residues processed: 332 average time/residue: 0.2652 time to fit residues: 142.4885 Evaluate side-chains 320 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 245 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 232 LEU 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 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 271 ILE 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 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 89 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 187 PHE 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 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 133 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 195 TYR Chi-restraints excluded: chain D residue 202 SER 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 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 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 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 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 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 248 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 7 optimal weight: 0.0060 chunk 177 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS G 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.232216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.184717 restraints weight = 24264.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.182068 restraints weight = 39773.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.184532 restraints weight = 30956.647| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20014 Z= 0.129 Angle : 0.676 9.569 27193 Z= 0.316 Chirality : 0.037 0.246 3205 Planarity : 0.004 0.040 3316 Dihedral : 4.316 21.280 2799 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.52 % Favored : 94.14 % Rotamer: Outliers : 4.97 % Allowed : 25.92 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.18), residues: 2408 helix: 1.94 (0.13), residues: 1736 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 345 HIS 0.002 0.000 HIS F 254 PHE 0.015 0.001 PHE C 269 TYR 0.009 0.001 TYR A 280 ARG 0.006 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 7) link_NAG-ASN : angle 5.22523 ( 21) hydrogen bonds : bond 0.03757 ( 1265) hydrogen bonds : angle 3.59641 ( 3753) SS BOND : bond 0.00856 ( 14) SS BOND : angle 1.88092 ( 28) covalent geometry : bond 0.00286 (19993) covalent geometry : angle 0.65809 (27144) *********************** 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 364 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 257 time to evaluate : 2.012 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: symmetry clash REVERT: A 323 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8032 (tp) REVERT: B 128 TRP cc_start: 0.8077 (OUTLIER) cc_final: 0.7807 (t-100) REVERT: C 101 MET cc_start: 0.4039 (ppp) cc_final: 0.3656 (ppp) REVERT: C 122 TYR cc_start: 0.8085 (t80) cc_final: 0.7840 (t80) REVERT: D 128 TRP cc_start: 0.7996 (OUTLIER) cc_final: 0.7418 (t-100) REVERT: D 337 ILE cc_start: 0.8142 (tt) cc_final: 0.7832 (pt) REVERT: E 31 GLU cc_start: 0.7773 (pm20) cc_final: 0.7464 (tp30) REVERT: E 101 MET cc_start: 0.4126 (tpp) cc_final: 0.3788 (tpp) REVERT: G 283 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.6891 (mp) outliers start: 107 outliers final: 84 residues processed: 337 average time/residue: 0.2680 time to fit residues: 146.1815 Evaluate side-chains 337 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 249 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 73 SER 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 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 271 ILE 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 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 217 LEU 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 C residue 342 SER 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 187 PHE Chi-restraints excluded: chain D residue 195 TYR 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 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 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 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 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 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 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 125 optimal weight: 0.6980 chunk 195 optimal weight: 0.9990 chunk 182 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 148 optimal weight: 0.1980 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS G 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.231605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184883 restraints weight = 24279.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.181879 restraints weight = 40504.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.184401 restraints weight = 32500.825| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2714 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= 0.133 Angle : 0.688 10.074 27193 Z= 0.320 Chirality : 0.037 0.226 3205 Planarity : 0.004 0.040 3316 Dihedral : 4.210 22.158 2799 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.56 % Favored : 94.10 % Rotamer: Outliers : 5.02 % Allowed : 26.38 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.18), residues: 2408 helix: 2.15 (0.12), residues: 1694 sheet: None (None), residues: 0 loop : -1.58 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 345 HIS 0.002 0.000 HIS F 254 PHE 0.016 0.001 PHE E 269 TYR 0.015 0.001 TYR F 186 ARG 0.006 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 7) link_NAG-ASN : angle 5.01194 ( 21) hydrogen bonds : bond 0.03775 ( 1265) hydrogen bonds : angle 3.58655 ( 3753) SS BOND : bond 0.00848 ( 14) SS BOND : angle 1.93803 ( 28) covalent geometry : bond 0.00301 (19993) covalent geometry : angle 0.67170 (27144) *********************** 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 363 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 255 time to evaluate : 2.148 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: 0.8384 (OUTLIER) cc_final: 0.8064 (tp) REVERT: B 128 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7769 (t-100) REVERT: C 101 MET cc_start: 0.4050 (ppp) cc_final: 0.3679 (ppp) REVERT: C 122 TYR cc_start: 0.8049 (t80) cc_final: 0.7849 (t80) REVERT: D 128 TRP cc_start: 0.7977 (OUTLIER) cc_final: 0.7353 (t-100) REVERT: D 337 ILE cc_start: 0.8021 (tt) cc_final: 0.7799 (pt) REVERT: E 31 GLU cc_start: 0.7866 (pm20) cc_final: 0.7361 (tp30) REVERT: E 101 MET cc_start: 0.3976 (tpp) cc_final: 0.3627 (tpp) REVERT: E 276 SER cc_start: 0.8064 (OUTLIER) cc_final: 0.7815 (m) REVERT: E 283 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.6768 (mp) REVERT: G 248 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6690 (pp) REVERT: G 283 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.6854 (mp) outliers start: 108 outliers final: 88 residues processed: 335 average time/residue: 0.2574 time to fit residues: 140.5631 Evaluate side-chains 342 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 247 time to evaluate : 2.136 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain A residue 128 TRP 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 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 271 ILE 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 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 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 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 128 TRP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 195 TYR 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 277 VAL 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 271 ILE Chi-restraints excluded: chain E residue 276 SER 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 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 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 248 LEU Chi-restraints excluded: chain G residue 260 THR 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 66 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 159 optimal weight: 0.2980 chunk 140 optimal weight: 30.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 237 GLN E 254 HIS G 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.220580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.180783 restraints weight = 23364.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.179246 restraints weight = 41795.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.181104 restraints weight = 34853.077| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2778 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 : 0.717 10.880 27193 Z= 0.336 Chirality : 0.039 0.211 3205 Planarity : 0.004 0.041 3316 Dihedral : 4.212 21.502 2799 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.52 % Favored : 94.14 % Rotamer: Outliers : 5.16 % Allowed : 26.34 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2408 helix: 2.06 (0.12), residues: 1694 sheet: -3.17 (0.43), residues: 70 loop : -1.38 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 85 HIS 0.002 0.001 HIS B 254 PHE 0.015 0.001 PHE C 269 TYR 0.016 0.001 TYR A 186 ARG 0.005 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 7) link_NAG-ASN : angle 5.29076 ( 21) hydrogen bonds : bond 0.04198 ( 1265) hydrogen bonds : angle 3.71426 ( 3753) SS BOND : bond 0.00863 ( 14) SS BOND : angle 2.29117 ( 28) covalent geometry : bond 0.00383 (19993) covalent geometry : angle 0.69898 (27144) *********************** 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 366 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 255 time to evaluate : 1.909 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: 0.8378 (OUTLIER) cc_final: 0.8101 (tp) REVERT: B 101 MET cc_start: 0.4433 (tpp) cc_final: 0.4142 (tpp) REVERT: B 128 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.7909 (t-100) REVERT: B 263 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8082 (pt) REVERT: C 101 MET cc_start: 0.4495 (ppp) cc_final: 0.3986 (ppp) REVERT: D 128 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7640 (t-100) REVERT: D 283 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7468 (mt) REVERT: E 31 GLU cc_start: 0.7867 (pm20) cc_final: 0.7357 (tp30) REVERT: E 101 MET cc_start: 0.4337 (tpp) cc_final: 0.4054 (tpp) REVERT: E 276 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7782 (m) REVERT: E 283 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7479 (mt) REVERT: F 122 TYR cc_start: 0.8044 (t80) cc_final: 0.7837 (t80) outliers start: 111 outliers final: 94 residues processed: 342 average time/residue: 0.3238 time to fit residues: 181.0410 Evaluate side-chains 349 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 248 time to evaluate : 2.784 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 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 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 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 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 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 128 TRP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 195 TYR 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 277 VAL Chi-restraints excluded: chain D residue 283 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 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 271 ILE 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 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 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 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 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 141 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS G 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.223020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.181074 restraints weight = 23324.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.179875 restraints weight = 38078.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.181984 restraints weight = 30531.613| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20014 Z= 0.143 Angle : 0.707 11.721 27193 Z= 0.330 Chirality : 0.038 0.199 3205 Planarity : 0.004 0.040 3316 Dihedral : 4.160 22.534 2799 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.32 % Favored : 94.35 % Rotamer: Outliers : 5.06 % Allowed : 26.38 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2408 helix: 2.07 (0.12), residues: 1694 sheet: -3.12 (0.45), residues: 70 loop : -1.37 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 345 HIS 0.002 0.001 HIS F 254 PHE 0.015 0.001 PHE D 269 TYR 0.011 0.001 TYR A 280 ARG 0.006 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 7) link_NAG-ASN : angle 4.94610 ( 21) hydrogen bonds : bond 0.03983 ( 1265) hydrogen bonds : angle 3.66458 ( 3753) SS BOND : bond 0.00856 ( 14) SS BOND : angle 2.18860 ( 28) covalent geometry : bond 0.00332 (19993) covalent geometry : angle 0.69043 (27144) *********************** 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 362 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 253 time to evaluate : 3.233 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: 0.8322 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 101 MET cc_start: 0.4049 (tpp) cc_final: 0.3832 (tpp) REVERT: B 128 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.7828 (t-100) REVERT: C 101 MET cc_start: 0.4373 (ppp) cc_final: 0.3872 (ppp) REVERT: C 126 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8001 (tp) REVERT: D 128 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.7569 (t-100) REVERT: D 283 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7384 (mt) REVERT: E 276 SER cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (m) REVERT: E 283 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.6769 (mp) REVERT: F 122 TYR cc_start: 0.8008 (t80) cc_final: 0.7743 (t80) outliers start: 109 outliers final: 96 residues processed: 336 average time/residue: 0.3614 time to fit residues: 201.9200 Evaluate side-chains 351 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 248 time to evaluate : 3.399 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 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 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 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 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 128 TRP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 195 TYR 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 283 LEU Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 68 SER 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 271 ILE 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 210 optimal weight: 40.0000 chunk 104 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 53 optimal weight: 0.0670 chunk 163 optimal weight: 3.9990 chunk 238 optimal weight: 0.0000 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS G 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.221962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.181947 restraints weight = 23334.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.180472 restraints weight = 37793.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.182292 restraints weight = 34026.106| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20014 Z= 0.152 Angle : 0.721 11.762 27193 Z= 0.336 Chirality : 0.039 0.190 3205 Planarity : 0.004 0.041 3316 Dihedral : 4.117 21.300 2799 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.61 % Favored : 94.06 % Rotamer: Outliers : 5.06 % Allowed : 26.43 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.18), residues: 2408 helix: 2.05 (0.12), residues: 1694 sheet: -3.01 (0.46), residues: 70 loop : -1.39 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 85 HIS 0.002 0.001 HIS B 254 PHE 0.015 0.001 PHE F 269 TYR 0.011 0.001 TYR A 280 ARG 0.005 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 7) link_NAG-ASN : angle 4.90945 ( 21) hydrogen bonds : bond 0.04083 ( 1265) hydrogen bonds : angle 3.70169 ( 3753) SS BOND : bond 0.00859 ( 14) SS BOND : angle 2.28613 ( 28) covalent geometry : bond 0.00358 (19993) covalent geometry : angle 0.70484 (27144) ********************** 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 363 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 254 time to evaluate : 3.056 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 50 MET cc_start: 0.7573 (ttm) cc_final: 0.7336 (ttt) REVERT: A 323 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8083 (tp) REVERT: B 128 TRP cc_start: 0.8147 (OUTLIER) cc_final: 0.7825 (t-100) REVERT: B 263 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8070 (pt) REVERT: C 101 MET cc_start: 0.4543 (ppp) cc_final: 0.4045 (ppp) REVERT: C 126 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7978 (tp) REVERT: C 159 GLN cc_start: 0.6135 (mp10) cc_final: 0.5670 (mp10) REVERT: C 201 ARG cc_start: 0.7489 (ptp-170) cc_final: 0.7197 (ptp90) REVERT: D 128 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7596 (t-100) REVERT: D 283 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7448 (mt) REVERT: E 276 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7869 (m) REVERT: E 283 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7478 (mt) REVERT: F 122 TYR cc_start: 0.8063 (t80) cc_final: 0.7840 (t80) outliers start: 109 outliers final: 98 residues processed: 334 average time/residue: 0.3477 time to fit residues: 193.9469 Evaluate side-chains 356 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 250 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 191 LEU 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 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 157 LEU 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 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 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 187 PHE Chi-restraints excluded: chain D residue 195 TYR 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 283 LEU Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 68 SER 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 271 ILE 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 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 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 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 271 ILE Chi-restraints excluded: chain G residue 277 VAL Chi-restraints excluded: chain G residue 337 ILE 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 195 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 156 optimal weight: 0.0050 chunk 134 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.228252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.182312 restraints weight = 24372.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.180205 restraints weight = 39626.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.182493 restraints weight = 34932.276| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20014 Z= 0.162 Angle : 0.740 11.992 27193 Z= 0.344 Chirality : 0.039 0.189 3205 Planarity : 0.004 0.041 3316 Dihedral : 4.171 21.578 2799 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.44 % Favored : 94.27 % Rotamer: Outliers : 5.29 % Allowed : 26.47 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.18), residues: 2408 helix: 2.02 (0.12), residues: 1694 sheet: -2.93 (0.46), residues: 70 loop : -1.40 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 85 HIS 0.002 0.001 HIS F 254 PHE 0.016 0.001 PHE G 269 TYR 0.016 0.001 TYR G 130 ARG 0.005 0.000 ARG B 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 7) link_NAG-ASN : angle 4.92708 ( 21) hydrogen bonds : bond 0.04199 ( 1265) hydrogen bonds : angle 3.74009 ( 3753) SS BOND : bond 0.00856 ( 14) SS BOND : angle 2.37823 ( 28) covalent geometry : bond 0.00388 (19993) covalent geometry : angle 0.72394 (27144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6176.27 seconds wall clock time: 113 minutes 27.32 seconds (6807.32 seconds total)