Starting phenix.real_space_refine on Thu Jun 19 19:21:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzm_26915/06_2025/7uzm_26915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzm_26915/06_2025/7uzm_26915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzm_26915/06_2025/7uzm_26915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzm_26915/06_2025/7uzm_26915.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzm_26915/06_2025/7uzm_26915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzm_26915/06_2025/7uzm_26915.cif" } resolution = 3.24 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= 0.001 sd= 0.039 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 108 5.16 5 C 14352 2.51 5 N 3996 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22752 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3787 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 13.42, per 1000 atoms: 0.59 Number of scatterers: 22752 At special positions: 0 Unit cell: (119.88, 112.32, 167.4, 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 108 16.00 O 4296 8.00 N 3996 7.00 C 14352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 3.1 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 59.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.631A pdb=" N VAL A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.611A pdb=" N SER A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.659A pdb=" N VAL A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 553 Processing helix chain 'B' and resid 65 through 89 removed outlier: 3.631A pdb=" N VAL B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 267 through 285 removed outlier: 4.413A pdb=" N THR B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 344 through 356 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 478 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.771A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 553 Processing helix chain 'C' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.736A pdb=" N MET C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.559A pdb=" N MET C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.909A pdb=" N ARG C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 553 Processing helix chain 'D' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 212 Processing helix chain 'D' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 267 through 285 removed outlier: 4.415A pdb=" N THR D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.561A pdb=" N MET D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 478 Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 501 through 528 removed outlier: 3.771A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 553 Processing helix chain 'E' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 94 removed outlier: 3.611A pdb=" N SER E 94 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.659A pdb=" N VAL E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 212 Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 324 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 391 through 396 removed outlier: 3.911A pdb=" N ARG E 395 " --> pdb=" O SER E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 421 Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 478 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 553 Processing helix chain 'F' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 212 Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.736A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 267 through 285 removed outlier: 4.413A pdb=" N THR F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 324 Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 370 through 374 Processing helix chain 'F' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG F 395 " --> pdb=" O SER F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 421 Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 478 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 553 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.687A pdb=" N GLY A 149 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY E 149 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE A 304 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY A 331 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 306 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE A 401 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 224 removed outlier: 3.687A pdb=" N GLY B 149 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 149 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 366 removed outlier: 6.692A pdb=" N PHE B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 401 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 220 through 224 removed outlier: 3.688A pdb=" N GLY C 149 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY F 149 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE C 304 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY C 331 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL C 306 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 401 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.692A pdb=" N PHE D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY D 331 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL D 306 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 401 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE E 401 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE F 304 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY F 331 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL F 306 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE F 401 " --> pdb=" O ILE F 425 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 4050 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: 8.46 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7631 1.34 - 1.46: 3653 1.46 - 1.58: 11767 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 23231 Sorted by residual: bond pdb=" C THR C 144 " pdb=" N PRO C 145 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.01e-02 9.80e+03 6.96e+00 bond pdb=" C THR F 144 " pdb=" N PRO F 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.78e+00 bond pdb=" C THR E 144 " pdb=" N PRO E 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.69e+00 bond pdb=" C THR B 144 " pdb=" N PRO B 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.63e+00 bond pdb=" C THR A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 1.333 1.359 -0.025 1.01e-02 9.80e+03 6.23e+00 ... (remaining 23226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 31042 2.33 - 4.66: 317 4.66 - 6.99: 30 6.99 - 9.32: 18 9.32 - 11.65: 6 Bond angle restraints: 31413 Sorted by residual: angle pdb=" N HIS F 142 " pdb=" CA HIS F 142 " pdb=" C HIS F 142 " ideal model delta sigma weight residual 111.07 102.28 8.79 1.07e+00 8.73e-01 6.75e+01 angle pdb=" N HIS C 142 " pdb=" CA HIS C 142 " pdb=" C HIS C 142 " ideal model delta sigma weight residual 111.07 102.37 8.70 1.07e+00 8.73e-01 6.61e+01 angle pdb=" N HIS B 142 " pdb=" CA HIS B 142 " pdb=" C HIS B 142 " ideal model delta sigma weight residual 111.07 102.56 8.51 1.07e+00 8.73e-01 6.32e+01 angle pdb=" N HIS E 142 " pdb=" CA HIS E 142 " pdb=" C HIS E 142 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.25e+01 angle pdb=" N HIS D 142 " pdb=" CA HIS D 142 " pdb=" C HIS D 142 " ideal model delta sigma weight residual 111.28 102.99 8.29 1.09e+00 8.42e-01 5.79e+01 ... (remaining 31408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 12662 16.11 - 32.21: 1032 32.21 - 48.32: 152 48.32 - 64.42: 42 64.42 - 80.52: 18 Dihedral angle restraints: 13906 sinusoidal: 5482 harmonic: 8424 Sorted by residual: dihedral pdb=" CA SER F 270 " pdb=" C SER F 270 " pdb=" N ALA F 271 " pdb=" CA ALA F 271 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER D 270 " pdb=" C SER D 270 " pdb=" N ALA D 271 " pdb=" CA ALA D 271 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER B 270 " pdb=" C SER B 270 " pdb=" N ALA B 271 " pdb=" CA ALA B 271 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 13903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2782 0.054 - 0.107: 555 0.107 - 0.161: 79 0.161 - 0.215: 4 0.215 - 0.268: 12 Chirality restraints: 3432 Sorted by residual: chirality pdb=" CA GLU D 552 " pdb=" N GLU D 552 " pdb=" C GLU D 552 " pdb=" CB GLU D 552 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA GLU A 552 " pdb=" N GLU A 552 " pdb=" C GLU A 552 " pdb=" CB GLU A 552 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE C 401 " pdb=" CA ILE C 401 " pdb=" CG1 ILE C 401 " pdb=" CG2 ILE C 401 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3429 not shown) Planarity restraints: 4121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 141 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C GLN D 141 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN D 141 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS D 142 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 141 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLN A 141 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A 141 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS A 142 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 258 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 259 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.025 5.00e-02 4.00e+02 ... (remaining 4118 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7478 2.84 - 3.36: 23379 3.36 - 3.87: 38561 3.87 - 4.39: 43906 4.39 - 4.90: 73975 Nonbonded interactions: 187299 Sorted by model distance: nonbonded pdb=" OD1 ASN E 392 " pdb=" NH2 ARG E 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN C 392 " pdb=" NH2 ARG C 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN D 392 " pdb=" NH2 ARG D 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN F 392 " pdb=" NH2 ARG F 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN A 392 " pdb=" NH2 ARG A 395 " model vdw 2.330 3.120 ... (remaining 187294 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 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'B' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'C' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'D' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'E' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 52.150 Find NCS groups from input model: 1.080 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 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 0.031 23231 Z= 0.158 Angle : 0.636 11.648 31413 Z= 0.381 Chirality : 0.044 0.268 3432 Planarity : 0.004 0.045 4121 Dihedral : 12.389 80.525 8542 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.59 (0.15), residues: 2952 helix: 2.27 (0.13), residues: 1542 sheet: 0.11 (0.25), residues: 372 loop : -0.43 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 338 HIS 0.003 0.001 HIS F 315 PHE 0.017 0.002 PHE B 67 TYR 0.010 0.001 TYR B 240 ARG 0.005 0.000 ARG E 101 Details of bonding type rmsd hydrogen bonds : bond 0.14589 ( 1416) hydrogen bonds : angle 5.36260 ( 4050) covalent geometry : bond 0.00276 (23231) covalent geometry : angle 0.63644 (31413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.7857 (tp) cc_final: 0.7549 (tp) REVERT: A 326 LYS cc_start: 0.7187 (ptpp) cc_final: 0.6966 (ptmt) REVERT: A 349 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7166 (mt-10) REVERT: A 412 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8336 (pm20) REVERT: A 471 GLN cc_start: 0.7407 (tt0) cc_final: 0.6808 (tp40) REVERT: A 495 ASP cc_start: 0.7209 (m-30) cc_final: 0.6934 (m-30) REVERT: B 238 ASP cc_start: 0.7071 (t0) cc_final: 0.6845 (t0) REVERT: B 309 PHE cc_start: 0.4447 (t80) cc_final: 0.4074 (t80) REVERT: B 412 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8305 (pm20) REVERT: B 468 MET cc_start: 0.6197 (ttp) cc_final: 0.5929 (ttp) REVERT: B 472 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 495 ASP cc_start: 0.7035 (m-30) cc_final: 0.6566 (m-30) REVERT: B 550 TYR cc_start: 0.8209 (t80) cc_final: 0.7896 (t80) REVERT: C 188 ILE cc_start: 0.7507 (tp) cc_final: 0.7095 (tp) REVERT: C 204 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7822 (tpt90) REVERT: C 215 ILE cc_start: 0.8551 (tt) cc_final: 0.8331 (tt) REVERT: C 314 LEU cc_start: 0.8258 (tp) cc_final: 0.7845 (tp) REVERT: C 349 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7251 (mt-10) REVERT: C 412 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8416 (pm20) REVERT: C 495 ASP cc_start: 0.7208 (m-30) cc_final: 0.6913 (m-30) REVERT: D 258 LYS cc_start: 0.7355 (mttt) cc_final: 0.7119 (mtpp) REVERT: D 314 LEU cc_start: 0.7761 (tp) cc_final: 0.7328 (tp) REVERT: D 349 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7147 (mt-10) REVERT: D 412 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8494 (pm20) REVERT: D 471 GLN cc_start: 0.7496 (tt0) cc_final: 0.6905 (tp40) REVERT: D 495 ASP cc_start: 0.7221 (m-30) cc_final: 0.6962 (m-30) REVERT: E 170 TYR cc_start: 0.7180 (m-10) cc_final: 0.6969 (m-10) REVERT: E 238 ASP cc_start: 0.7103 (t0) cc_final: 0.6885 (t0) REVERT: E 309 PHE cc_start: 0.4480 (t80) cc_final: 0.4105 (t80) REVERT: E 317 MET cc_start: 0.6802 (ptm) cc_final: 0.6596 (ptt) REVERT: E 412 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8288 (pm20) REVERT: E 495 ASP cc_start: 0.6955 (m-30) cc_final: 0.6584 (m-30) REVERT: E 550 TYR cc_start: 0.8195 (t80) cc_final: 0.7893 (t80) REVERT: F 188 ILE cc_start: 0.7585 (tp) cc_final: 0.7260 (tp) REVERT: F 204 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7927 (tpt90) REVERT: F 215 ILE cc_start: 0.8559 (tt) cc_final: 0.8332 (tt) REVERT: F 314 LEU cc_start: 0.8252 (tp) cc_final: 0.7856 (tp) REVERT: F 317 MET cc_start: 0.6908 (ptm) cc_final: 0.6707 (ptt) REVERT: F 347 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8564 (tm-30) REVERT: F 349 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7131 (mt-10) REVERT: F 412 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8375 (mp0) REVERT: F 495 ASP cc_start: 0.7231 (m-30) cc_final: 0.6992 (m-30) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.3850 time to fit residues: 351.2099 Evaluate side-chains 362 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 230 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 262 GLN B 262 GLN ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 262 GLN D 189 ASN D 262 GLN E 262 GLN ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 ASN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN F 262 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137762 restraints weight = 28982.985| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.54 r_work: 0.3426 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23231 Z= 0.156 Angle : 0.592 9.886 31413 Z= 0.311 Chirality : 0.046 0.222 3432 Planarity : 0.004 0.036 4121 Dihedral : 4.390 16.313 3228 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.69 % Allowed : 10.79 % Favored : 86.52 % 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 (0.16), residues: 2952 helix: 2.17 (0.13), residues: 1596 sheet: 0.33 (0.26), residues: 366 loop : -0.71 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 338 HIS 0.006 0.001 HIS F 507 PHE 0.028 0.002 PHE C 304 TYR 0.017 0.002 TYR D 528 ARG 0.005 0.001 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04744 ( 1416) hydrogen bonds : angle 4.15167 ( 4050) covalent geometry : bond 0.00366 (23231) covalent geometry : angle 0.59151 (31413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 382 time to evaluate : 2.428 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 252 HIS cc_start: 0.8281 (t-170) cc_final: 0.8061 (t-170) REVERT: A 262 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7568 (mm110) REVERT: A 266 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7041 (m-70) REVERT: A 281 GLU cc_start: 0.7880 (tp30) cc_final: 0.7410 (tp30) REVERT: A 314 LEU cc_start: 0.8193 (tp) cc_final: 0.7962 (tp) REVERT: A 338 TRP cc_start: 0.7690 (t-100) cc_final: 0.7395 (t-100) REVERT: A 399 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7098 (mttm) REVERT: A 495 ASP cc_start: 0.7837 (m-30) cc_final: 0.7499 (m-30) REVERT: B 326 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7138 (mttp) REVERT: B 349 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7049 (mp0) REVERT: B 399 LYS cc_start: 0.7779 (mmmt) cc_final: 0.7440 (mttm) REVERT: B 468 MET cc_start: 0.7473 (ttp) cc_final: 0.7261 (ttp) REVERT: B 472 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7700 (mm-30) REVERT: B 495 ASP cc_start: 0.7708 (m-30) cc_final: 0.7220 (m-30) REVERT: C 207 MET cc_start: 0.8262 (mtm) cc_final: 0.8007 (mtm) REVERT: C 252 HIS cc_start: 0.8298 (t-170) cc_final: 0.8082 (t-170) REVERT: C 281 GLU cc_start: 0.7707 (tp30) cc_final: 0.7371 (tp30) REVERT: C 282 ASN cc_start: 0.8340 (m-40) cc_final: 0.8005 (m110) REVERT: C 349 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7247 (mt-10) REVERT: C 373 GLU cc_start: 0.7346 (mp0) cc_final: 0.6939 (mp0) REVERT: C 399 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7185 (tttm) REVERT: D 66 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.5133 (m-10) REVERT: D 69 MET cc_start: 0.7147 (mtt) cc_final: 0.6839 (mtt) REVERT: D 252 HIS cc_start: 0.8341 (t-170) cc_final: 0.8126 (t-170) REVERT: D 266 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.7192 (m-70) REVERT: D 281 GLU cc_start: 0.7493 (tp30) cc_final: 0.6988 (tp30) REVERT: D 314 LEU cc_start: 0.8126 (tp) cc_final: 0.7827 (tp) REVERT: D 338 TRP cc_start: 0.7732 (t-100) cc_final: 0.7522 (t-100) REVERT: D 399 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7104 (mttt) REVERT: D 495 ASP cc_start: 0.7811 (m-30) cc_final: 0.7479 (m-30) REVERT: E 349 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7080 (mp0) REVERT: E 399 LYS cc_start: 0.7770 (mmmt) cc_final: 0.7442 (mttm) REVERT: E 472 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7619 (mm-30) REVERT: E 495 ASP cc_start: 0.7809 (m-30) cc_final: 0.7330 (m-30) REVERT: F 66 PHE cc_start: 0.6553 (m-80) cc_final: 0.6043 (m-80) REVERT: F 207 MET cc_start: 0.8299 (mtm) cc_final: 0.8033 (mtm) REVERT: F 252 HIS cc_start: 0.8250 (t-170) cc_final: 0.8028 (t-170) REVERT: F 281 GLU cc_start: 0.7695 (tp30) cc_final: 0.7395 (tp30) REVERT: F 282 ASN cc_start: 0.8289 (m-40) cc_final: 0.7915 (m110) REVERT: F 314 LEU cc_start: 0.8452 (tp) cc_final: 0.8086 (tp) REVERT: F 349 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7249 (mt-10) REVERT: F 373 GLU cc_start: 0.7394 (mp0) cc_final: 0.7046 (mp0) REVERT: F 399 LYS cc_start: 0.7559 (mmmt) cc_final: 0.7012 (tttm) REVERT: F 472 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7678 (mm-30) outliers start: 64 outliers final: 31 residues processed: 416 average time/residue: 0.3518 time to fit residues: 227.1627 Evaluate side-chains 359 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 324 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 245 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 212 optimal weight: 0.3980 chunk 76 optimal weight: 8.9990 chunk 287 optimal weight: 0.0870 chunk 5 optimal weight: 0.0570 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 448 HIS ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 262 GLN D 189 ASN ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 ASN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN F 262 GLN F 448 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.183555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141351 restraints weight = 28873.334| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.44 r_work: 0.3505 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 23231 Z= 0.106 Angle : 0.528 11.039 31413 Z= 0.269 Chirality : 0.042 0.171 3432 Planarity : 0.004 0.034 4121 Dihedral : 4.107 19.996 3228 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.89 % Allowed : 14.07 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.15), residues: 2952 helix: 2.27 (0.13), residues: 1596 sheet: 0.32 (0.26), residues: 366 loop : -0.79 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 338 HIS 0.008 0.001 HIS D 142 PHE 0.028 0.002 PHE C 304 TYR 0.015 0.001 TYR B 528 ARG 0.007 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 1416) hydrogen bonds : angle 3.90756 ( 4050) covalent geometry : bond 0.00240 (23231) covalent geometry : angle 0.52789 (31413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 377 time to evaluate : 2.376 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 67 PHE cc_start: 0.6507 (m-10) cc_final: 0.5667 (m-10) REVERT: A 143 ARG cc_start: 0.8272 (mmm160) cc_final: 0.6589 (mpt-90) REVERT: A 252 HIS cc_start: 0.8325 (t-170) cc_final: 0.8089 (t-170) REVERT: A 266 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7151 (m-70) REVERT: A 281 GLU cc_start: 0.7874 (tp30) cc_final: 0.7418 (tp30) REVERT: A 282 ASN cc_start: 0.8208 (m-40) cc_final: 0.7765 (m110) REVERT: A 309 PHE cc_start: 0.6336 (t80) cc_final: 0.6067 (t80) REVERT: A 326 LYS cc_start: 0.8310 (mttp) cc_final: 0.7529 (ptmt) REVERT: A 338 TRP cc_start: 0.7678 (t-100) cc_final: 0.7300 (t-100) REVERT: A 370 SER cc_start: 0.6972 (OUTLIER) cc_final: 0.6584 (t) REVERT: A 387 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6514 (mm110) REVERT: A 399 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7240 (mttm) REVERT: A 495 ASP cc_start: 0.7976 (m-30) cc_final: 0.7688 (m-30) REVERT: B 262 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7067 (mp10) REVERT: B 282 ASN cc_start: 0.8223 (m-40) cc_final: 0.7777 (m110) REVERT: B 326 LYS cc_start: 0.7897 (mtpt) cc_final: 0.7525 (mtpt) REVERT: B 399 LYS cc_start: 0.7850 (mmmt) cc_final: 0.7578 (mttm) REVERT: B 468 MET cc_start: 0.7500 (ttp) cc_final: 0.7199 (ttp) REVERT: B 472 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 495 ASP cc_start: 0.7831 (m-30) cc_final: 0.7357 (m-30) REVERT: C 207 MET cc_start: 0.8421 (mtm) cc_final: 0.8125 (mtm) REVERT: C 252 HIS cc_start: 0.8376 (t-170) cc_final: 0.8158 (t-170) REVERT: C 281 GLU cc_start: 0.7720 (tp30) cc_final: 0.7389 (tp30) REVERT: C 282 ASN cc_start: 0.8405 (m-40) cc_final: 0.7955 (m110) REVERT: C 349 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7281 (mt-10) REVERT: C 373 GLU cc_start: 0.7214 (mp0) cc_final: 0.6894 (mp0) REVERT: C 399 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7244 (mttm) REVERT: D 66 PHE cc_start: 0.5660 (OUTLIER) cc_final: 0.5249 (m-10) REVERT: D 67 PHE cc_start: 0.6651 (m-10) cc_final: 0.5747 (m-10) REVERT: D 252 HIS cc_start: 0.8438 (t-170) cc_final: 0.8211 (t-170) REVERT: D 266 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.7157 (m-70) REVERT: D 281 GLU cc_start: 0.7445 (tp30) cc_final: 0.7049 (tp30) REVERT: D 282 ASN cc_start: 0.8240 (m-40) cc_final: 0.7796 (m110) REVERT: D 326 LYS cc_start: 0.8471 (mttp) cc_final: 0.7624 (ptmt) REVERT: D 338 TRP cc_start: 0.7729 (t-100) cc_final: 0.7487 (t-100) REVERT: D 370 SER cc_start: 0.7017 (OUTLIER) cc_final: 0.6666 (t) REVERT: D 399 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7251 (mttt) REVERT: D 495 ASP cc_start: 0.7934 (m-30) cc_final: 0.7590 (m-30) REVERT: E 262 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7020 (mp10) REVERT: E 282 ASN cc_start: 0.8206 (m-40) cc_final: 0.7801 (m110) REVERT: E 349 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7142 (mp0) REVERT: E 399 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7593 (mttm) REVERT: E 472 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7671 (mm-30) REVERT: E 495 ASP cc_start: 0.7875 (m-30) cc_final: 0.7374 (m-30) REVERT: F 207 MET cc_start: 0.8486 (mtm) cc_final: 0.8208 (mtm) REVERT: F 252 HIS cc_start: 0.8293 (t-170) cc_final: 0.8088 (t-170) REVERT: F 281 GLU cc_start: 0.7732 (tp30) cc_final: 0.7400 (tp30) REVERT: F 282 ASN cc_start: 0.8398 (m-40) cc_final: 0.7933 (m110) REVERT: F 309 PHE cc_start: 0.5898 (t80) cc_final: 0.5615 (t80) REVERT: F 326 LYS cc_start: 0.7430 (ptmt) cc_final: 0.6661 (mtmt) REVERT: F 349 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7334 (mt-10) REVERT: F 373 GLU cc_start: 0.7318 (mp0) cc_final: 0.7016 (mp0) REVERT: F 399 LYS cc_start: 0.7628 (mmmt) cc_final: 0.7135 (mttm) REVERT: F 472 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7698 (mm-30) outliers start: 45 outliers final: 25 residues processed: 397 average time/residue: 0.3536 time to fit residues: 220.0352 Evaluate side-chains 357 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 111 optimal weight: 0.9980 chunk 258 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 42 optimal weight: 0.0050 chunk 184 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 262 GLN B 189 ASN B 262 GLN C 189 ASN C 262 GLN D 189 ASN E 189 ASN E 262 GLN F 189 ASN F 262 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.181783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144428 restraints weight = 29440.741| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.94 r_work: 0.3488 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23231 Z= 0.115 Angle : 0.520 10.888 31413 Z= 0.266 Chirality : 0.043 0.161 3432 Planarity : 0.004 0.029 4121 Dihedral : 4.033 19.290 3228 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.32 % Allowed : 14.70 % Favored : 81.98 % 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: 1.54 (0.15), residues: 2952 helix: 2.30 (0.13), residues: 1596 sheet: 0.29 (0.27), residues: 366 loop : -0.85 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 338 HIS 0.007 0.001 HIS D 142 PHE 0.029 0.002 PHE C 304 TYR 0.016 0.001 TYR A 528 ARG 0.005 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 1416) hydrogen bonds : angle 3.86961 ( 4050) covalent geometry : bond 0.00269 (23231) covalent geometry : angle 0.51996 (31413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6187 (m-10) cc_final: 0.5500 (m-10) REVERT: A 266 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.7232 (m-70) REVERT: A 281 GLU cc_start: 0.8096 (tp30) cc_final: 0.7703 (tp30) REVERT: A 282 ASN cc_start: 0.8144 (m-40) cc_final: 0.7789 (m110) REVERT: A 326 LYS cc_start: 0.8288 (mttp) cc_final: 0.7603 (ptmt) REVERT: A 338 TRP cc_start: 0.7544 (t-100) cc_final: 0.7092 (t-100) REVERT: A 370 SER cc_start: 0.6891 (OUTLIER) cc_final: 0.6459 (t) REVERT: A 373 GLU cc_start: 0.7216 (mp0) cc_final: 0.6657 (pm20) REVERT: A 387 GLN cc_start: 0.6763 (OUTLIER) cc_final: 0.6460 (mm110) REVERT: A 399 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7325 (mttm) REVERT: A 495 ASP cc_start: 0.8118 (m-30) cc_final: 0.7730 (m-30) REVERT: B 141 GLN cc_start: 0.7466 (mp10) cc_final: 0.7216 (mp10) REVERT: B 282 ASN cc_start: 0.8281 (m-40) cc_final: 0.7935 (m110) REVERT: B 326 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7686 (mtpt) REVERT: B 349 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7180 (mt-10) REVERT: B 387 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6353 (mm110) REVERT: B 472 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 495 ASP cc_start: 0.8055 (m-30) cc_final: 0.7555 (m-30) REVERT: C 67 PHE cc_start: 0.6024 (m-10) cc_final: 0.5666 (t80) REVERT: C 233 MET cc_start: 0.8361 (mmm) cc_final: 0.8127 (mmt) REVERT: C 281 GLU cc_start: 0.8047 (tp30) cc_final: 0.7789 (tp30) REVERT: C 282 ASN cc_start: 0.8388 (m-40) cc_final: 0.8042 (m110) REVERT: C 295 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6562 (ptt) REVERT: C 387 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6354 (mm-40) REVERT: D 66 PHE cc_start: 0.5674 (m-80) cc_final: 0.5252 (m-10) REVERT: D 67 PHE cc_start: 0.6228 (m-10) cc_final: 0.5553 (m-10) REVERT: D 266 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.7247 (m-70) REVERT: D 281 GLU cc_start: 0.7836 (tp30) cc_final: 0.7626 (tp30) REVERT: D 282 ASN cc_start: 0.8227 (m-40) cc_final: 0.7910 (m110) REVERT: D 326 LYS cc_start: 0.8356 (mttp) cc_final: 0.7544 (ptmt) REVERT: D 338 TRP cc_start: 0.7630 (t-100) cc_final: 0.7310 (t-100) REVERT: D 370 SER cc_start: 0.6956 (OUTLIER) cc_final: 0.6656 (t) REVERT: D 373 GLU cc_start: 0.7405 (mp0) cc_final: 0.6911 (pm20) REVERT: D 399 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7366 (mttm) REVERT: D 495 ASP cc_start: 0.8120 (m-30) cc_final: 0.7732 (m-30) REVERT: E 67 PHE cc_start: 0.6173 (m-10) cc_final: 0.5599 (t80) REVERT: E 141 GLN cc_start: 0.7328 (mp10) cc_final: 0.7077 (mp10) REVERT: E 349 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7141 (mp0) REVERT: E 387 GLN cc_start: 0.6537 (OUTLIER) cc_final: 0.6298 (mm110) REVERT: E 472 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8097 (mm-30) REVERT: E 495 ASP cc_start: 0.8101 (m-30) cc_final: 0.7603 (m-30) REVERT: F 67 PHE cc_start: 0.5994 (m-10) cc_final: 0.5647 (t80) REVERT: F 281 GLU cc_start: 0.8062 (tp30) cc_final: 0.7767 (tp30) REVERT: F 282 ASN cc_start: 0.8349 (m-40) cc_final: 0.7996 (m110) REVERT: F 326 LYS cc_start: 0.7405 (ptmt) cc_final: 0.6721 (mtmt) REVERT: F 349 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7392 (mt-10) REVERT: F 387 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6510 (mm110) outliers start: 79 outliers final: 47 residues processed: 406 average time/residue: 0.3249 time to fit residues: 212.5932 Evaluate side-chains 374 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 317 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 53 optimal weight: 0.8980 chunk 283 optimal weight: 0.8980 chunk 140 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141612 restraints weight = 29201.097| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.99 r_work: 0.3470 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23231 Z= 0.115 Angle : 0.523 10.569 31413 Z= 0.266 Chirality : 0.042 0.148 3432 Planarity : 0.004 0.031 4121 Dihedral : 4.033 19.701 3228 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.15 % Allowed : 15.75 % Favored : 81.10 % 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: 1.54 (0.15), residues: 2952 helix: 2.33 (0.13), residues: 1596 sheet: 0.21 (0.26), residues: 366 loop : -0.87 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 338 HIS 0.003 0.001 HIS C 448 PHE 0.031 0.002 PHE F 304 TYR 0.015 0.001 TYR A 528 ARG 0.008 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1416) hydrogen bonds : angle 3.84807 ( 4050) covalent geometry : bond 0.00271 (23231) covalent geometry : angle 0.52326 (31413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 339 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5900 (m-10) cc_final: 0.5328 (m-10) REVERT: A 266 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.7046 (m-70) REVERT: A 281 GLU cc_start: 0.7760 (tp30) cc_final: 0.7428 (tp30) REVERT: A 282 ASN cc_start: 0.7964 (m-40) cc_final: 0.7591 (m110) REVERT: A 326 LYS cc_start: 0.8207 (mttp) cc_final: 0.7558 (ptmt) REVERT: A 338 TRP cc_start: 0.7445 (t-100) cc_final: 0.7079 (t-100) REVERT: A 370 SER cc_start: 0.6869 (OUTLIER) cc_final: 0.6408 (t) REVERT: A 387 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6618 (mm110) REVERT: A 399 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7425 (mttm) REVERT: A 495 ASP cc_start: 0.7936 (m-30) cc_final: 0.7535 (m-30) REVERT: B 282 ASN cc_start: 0.8153 (m-40) cc_final: 0.7802 (m110) REVERT: B 319 TYR cc_start: 0.7733 (m-80) cc_final: 0.7493 (m-80) REVERT: B 326 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7727 (mtpt) REVERT: B 387 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6343 (mm110) REVERT: B 472 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 495 ASP cc_start: 0.7813 (m-30) cc_final: 0.7294 (m-30) REVERT: C 207 MET cc_start: 0.8149 (mtm) cc_final: 0.7907 (mtm) REVERT: C 281 GLU cc_start: 0.7752 (tp30) cc_final: 0.7439 (tp30) REVERT: C 282 ASN cc_start: 0.8274 (m-40) cc_final: 0.7926 (m110) REVERT: C 295 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6611 (ptt) REVERT: C 387 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6627 (mm110) REVERT: C 399 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7447 (mttm) REVERT: C 412 GLU cc_start: 0.7648 (pm20) cc_final: 0.7277 (tm-30) REVERT: D 66 PHE cc_start: 0.5547 (OUTLIER) cc_final: 0.5185 (m-10) REVERT: D 67 PHE cc_start: 0.5853 (m-80) cc_final: 0.5348 (m-10) REVERT: D 266 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.7110 (m-70) REVERT: D 282 ASN cc_start: 0.7966 (m-40) cc_final: 0.7708 (m110) REVERT: D 326 LYS cc_start: 0.8281 (mttp) cc_final: 0.7598 (ptmt) REVERT: D 338 TRP cc_start: 0.7536 (t-100) cc_final: 0.7240 (t-100) REVERT: D 370 SER cc_start: 0.6854 (OUTLIER) cc_final: 0.6545 (t) REVERT: D 399 LYS cc_start: 0.7717 (mmmt) cc_final: 0.7362 (mttm) REVERT: D 495 ASP cc_start: 0.7942 (m-30) cc_final: 0.7535 (m-30) REVERT: E 387 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6469 (mm110) REVERT: E 472 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7807 (mm-30) REVERT: E 495 ASP cc_start: 0.7885 (m-30) cc_final: 0.7380 (m-30) REVERT: F 143 ARG cc_start: 0.8174 (mmm160) cc_final: 0.6949 (mpt-90) REVERT: F 207 MET cc_start: 0.8199 (mtm) cc_final: 0.7949 (mtm) REVERT: F 281 GLU cc_start: 0.7717 (tp30) cc_final: 0.7499 (tp30) REVERT: F 282 ASN cc_start: 0.8253 (m-40) cc_final: 0.7901 (m110) REVERT: F 326 LYS cc_start: 0.7348 (ptmt) cc_final: 0.6810 (mtmt) REVERT: F 387 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6599 (mm110) REVERT: F 399 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7374 (mttm) REVERT: F 412 GLU cc_start: 0.7582 (pm20) cc_final: 0.7239 (tm-30) outliers start: 75 outliers final: 52 residues processed: 378 average time/residue: 0.3286 time to fit residues: 199.2968 Evaluate side-chains 376 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 313 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 277 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 254 optimal weight: 0.0970 chunk 273 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 ASN C 262 GLN C 431 ASN D 142 HIS ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.184226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146125 restraints weight = 29352.298| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.14 r_work: 0.3520 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23231 Z= 0.110 Angle : 0.510 10.770 31413 Z= 0.260 Chirality : 0.042 0.147 3432 Planarity : 0.004 0.033 4121 Dihedral : 3.964 18.172 3228 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.53 % Allowed : 15.75 % Favored : 80.72 % 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 (0.15), residues: 2952 helix: 2.37 (0.13), residues: 1596 sheet: 0.07 (0.26), residues: 378 loop : -0.89 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 338 HIS 0.003 0.001 HIS D 252 PHE 0.034 0.001 PHE B 304 TYR 0.016 0.001 TYR A 528 ARG 0.005 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 1416) hydrogen bonds : angle 3.82096 ( 4050) covalent geometry : bond 0.00256 (23231) covalent geometry : angle 0.50996 (31413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 335 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5719 (m-80) cc_final: 0.5216 (m-10) REVERT: A 69 MET cc_start: 0.6973 (mmt) cc_final: 0.6483 (mmt) REVERT: A 281 GLU cc_start: 0.7719 (tp30) cc_final: 0.7375 (tp30) REVERT: A 282 ASN cc_start: 0.7935 (m-40) cc_final: 0.7544 (m110) REVERT: A 326 LYS cc_start: 0.8193 (mttp) cc_final: 0.7553 (ptmt) REVERT: A 338 TRP cc_start: 0.7360 (t-100) cc_final: 0.7048 (t-100) REVERT: A 387 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6666 (mm110) REVERT: A 399 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7425 (mttm) REVERT: A 495 ASP cc_start: 0.7886 (m-30) cc_final: 0.7459 (m-30) REVERT: B 319 TYR cc_start: 0.7833 (m-80) cc_final: 0.7555 (m-80) REVERT: B 326 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7674 (mtpt) REVERT: B 387 GLN cc_start: 0.6791 (OUTLIER) cc_final: 0.6540 (mm110) REVERT: B 423 MET cc_start: 0.7668 (ttt) cc_final: 0.7347 (ttm) REVERT: B 472 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7821 (mm-30) REVERT: B 495 ASP cc_start: 0.7798 (m-30) cc_final: 0.7259 (m-30) REVERT: B 533 ASP cc_start: 0.8539 (t0) cc_final: 0.8221 (t0) REVERT: C 207 MET cc_start: 0.8273 (mtm) cc_final: 0.8047 (mtm) REVERT: C 370 SER cc_start: 0.6461 (OUTLIER) cc_final: 0.5839 (t) REVERT: C 387 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6642 (mm110) REVERT: C 399 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7455 (mttt) REVERT: D 66 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.5158 (m-10) REVERT: D 67 PHE cc_start: 0.5691 (m-80) cc_final: 0.5192 (m-10) REVERT: D 266 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.7113 (m-70) REVERT: D 282 ASN cc_start: 0.7845 (m-40) cc_final: 0.7582 (m110) REVERT: D 326 LYS cc_start: 0.8238 (mttp) cc_final: 0.7580 (ptmt) REVERT: D 338 TRP cc_start: 0.7423 (t-100) cc_final: 0.7079 (t-100) REVERT: D 399 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7518 (mttm) REVERT: D 495 ASP cc_start: 0.7916 (m-30) cc_final: 0.7499 (m-30) REVERT: E 99 ARG cc_start: 0.7322 (mmm-85) cc_final: 0.6538 (mmm-85) REVERT: E 387 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6530 (mm110) REVERT: E 472 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7840 (mm-30) REVERT: E 495 ASP cc_start: 0.7791 (m-30) cc_final: 0.7295 (m-30) REVERT: E 533 ASP cc_start: 0.8567 (t0) cc_final: 0.8255 (t0) REVERT: F 207 MET cc_start: 0.8314 (mtm) cc_final: 0.8065 (mtm) REVERT: F 281 GLU cc_start: 0.7796 (tp30) cc_final: 0.7462 (tp30) REVERT: F 326 LYS cc_start: 0.7409 (ptmt) cc_final: 0.6893 (mtmt) REVERT: F 387 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6695 (mm110) REVERT: F 399 LYS cc_start: 0.7696 (mmmt) cc_final: 0.7473 (mttt) REVERT: F 533 ASP cc_start: 0.8520 (t0) cc_final: 0.7899 (t0) outliers start: 84 outliers final: 55 residues processed: 380 average time/residue: 0.3174 time to fit residues: 192.8681 Evaluate side-chains 373 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 310 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 64 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 206 optimal weight: 0.2980 chunk 49 optimal weight: 10.0000 chunk 232 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 247 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 262 GLN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144319 restraints weight = 29354.938| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.00 r_work: 0.3515 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23231 Z= 0.113 Angle : 0.510 10.920 31413 Z= 0.262 Chirality : 0.042 0.199 3432 Planarity : 0.004 0.032 4121 Dihedral : 3.952 16.983 3228 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.86 % Allowed : 15.46 % Favored : 80.68 % 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 (0.15), residues: 2952 helix: 2.34 (0.13), residues: 1596 sheet: -0.01 (0.26), residues: 378 loop : -0.92 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 338 HIS 0.003 0.001 HIS E 448 PHE 0.033 0.002 PHE F 304 TYR 0.014 0.001 TYR A 528 ARG 0.008 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1416) hydrogen bonds : angle 3.83721 ( 4050) covalent geometry : bond 0.00264 (23231) covalent geometry : angle 0.50967 (31413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 319 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5702 (m-80) cc_final: 0.5475 (t80) REVERT: A 69 MET cc_start: 0.7076 (mmt) cc_final: 0.6566 (mmt) REVERT: A 281 GLU cc_start: 0.7642 (tp30) cc_final: 0.7302 (tp30) REVERT: A 282 ASN cc_start: 0.7887 (m-40) cc_final: 0.7473 (m110) REVERT: A 326 LYS cc_start: 0.8220 (mttp) cc_final: 0.7574 (ptmt) REVERT: A 387 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6685 (mm110) REVERT: A 399 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7333 (mttm) REVERT: A 495 ASP cc_start: 0.7901 (m-30) cc_final: 0.7464 (m-30) REVERT: B 99 ARG cc_start: 0.7401 (mmm-85) cc_final: 0.6653 (mmm-85) REVERT: B 319 TYR cc_start: 0.7896 (m-80) cc_final: 0.7615 (m-80) REVERT: B 326 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7664 (mtpt) REVERT: B 387 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6495 (mm110) REVERT: B 423 MET cc_start: 0.7711 (ttt) cc_final: 0.7426 (ttm) REVERT: B 472 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 495 ASP cc_start: 0.7799 (m-30) cc_final: 0.7260 (m-30) REVERT: B 533 ASP cc_start: 0.8562 (t0) cc_final: 0.8252 (t0) REVERT: C 207 MET cc_start: 0.8272 (mtm) cc_final: 0.8042 (mtm) REVERT: C 387 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6740 (mm110) REVERT: C 412 GLU cc_start: 0.7657 (pm20) cc_final: 0.7301 (tm-30) REVERT: C 533 ASP cc_start: 0.8502 (t0) cc_final: 0.7878 (t0) REVERT: D 66 PHE cc_start: 0.5388 (OUTLIER) cc_final: 0.5112 (m-10) REVERT: D 67 PHE cc_start: 0.5765 (m-80) cc_final: 0.5244 (m-10) REVERT: D 281 GLU cc_start: 0.7895 (tp30) cc_final: 0.7483 (tp30) REVERT: D 282 ASN cc_start: 0.7796 (m-40) cc_final: 0.7552 (m110) REVERT: D 326 LYS cc_start: 0.8274 (mttp) cc_final: 0.7601 (ptmt) REVERT: D 338 TRP cc_start: 0.7352 (t-100) cc_final: 0.7025 (t-100) REVERT: D 495 ASP cc_start: 0.7922 (m-30) cc_final: 0.7473 (m-30) REVERT: E 99 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.6831 (mmm-85) REVERT: E 387 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6579 (mm110) REVERT: E 472 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7801 (mm-30) REVERT: E 495 ASP cc_start: 0.7814 (m-30) cc_final: 0.7300 (m-30) REVERT: E 533 ASP cc_start: 0.8501 (t0) cc_final: 0.8214 (t0) REVERT: F 207 MET cc_start: 0.8301 (mtm) cc_final: 0.8055 (mtm) REVERT: F 326 LYS cc_start: 0.7397 (ptmt) cc_final: 0.6839 (mtmt) REVERT: F 387 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6773 (mm110) REVERT: F 399 LYS cc_start: 0.7695 (mmmt) cc_final: 0.7478 (mttt) REVERT: F 412 GLU cc_start: 0.7562 (pm20) cc_final: 0.7263 (tm-30) REVERT: F 533 ASP cc_start: 0.8511 (t0) cc_final: 0.7896 (t0) outliers start: 92 outliers final: 63 residues processed: 374 average time/residue: 0.3481 time to fit residues: 206.8837 Evaluate side-chains 372 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 183 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 225 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 167 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 262 GLN C 282 ASN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 262 GLN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 448 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.176290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137576 restraints weight = 29603.185| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.93 r_work: 0.3422 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23231 Z= 0.189 Angle : 0.598 10.269 31413 Z= 0.312 Chirality : 0.046 0.235 3432 Planarity : 0.004 0.034 4121 Dihedral : 4.350 17.802 3228 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.82 % Allowed : 15.41 % Favored : 80.76 % 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: 1.16 (0.15), residues: 2952 helix: 2.10 (0.13), residues: 1560 sheet: 0.01 (0.26), residues: 366 loop : -1.06 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 338 HIS 0.004 0.001 HIS A 142 PHE 0.033 0.002 PHE F 304 TYR 0.017 0.002 TYR D 170 ARG 0.006 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 1416) hydrogen bonds : angle 4.16018 ( 4050) covalent geometry : bond 0.00456 (23231) covalent geometry : angle 0.59831 (31413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 289 time to evaluate : 2.428 Fit side-chains REVERT: A 67 PHE cc_start: 0.6003 (m-80) cc_final: 0.5503 (t80) REVERT: A 69 MET cc_start: 0.7452 (mmt) cc_final: 0.6903 (mmt) REVERT: A 282 ASN cc_start: 0.8201 (m-40) cc_final: 0.7953 (m110) REVERT: A 326 LYS cc_start: 0.8414 (mttp) cc_final: 0.7749 (ptmt) REVERT: A 397 LYS cc_start: 0.7781 (ptpt) cc_final: 0.7506 (tmtt) REVERT: A 399 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7314 (mttm) REVERT: A 495 ASP cc_start: 0.8235 (m-30) cc_final: 0.7813 (m-30) REVERT: B 319 TYR cc_start: 0.7933 (m-80) cc_final: 0.7564 (m-80) REVERT: B 387 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6996 (mm110) REVERT: B 472 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8123 (mm-30) REVERT: B 495 ASP cc_start: 0.8067 (m-30) cc_final: 0.7566 (m-30) REVERT: B 533 ASP cc_start: 0.8509 (t0) cc_final: 0.8201 (t0) REVERT: C 207 MET cc_start: 0.8625 (mtm) cc_final: 0.8398 (mtm) REVERT: C 387 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7199 (mm110) REVERT: C 533 ASP cc_start: 0.8711 (t0) cc_final: 0.8166 (t0) REVERT: D 66 PHE cc_start: 0.5738 (OUTLIER) cc_final: 0.5337 (m-80) REVERT: D 67 PHE cc_start: 0.6065 (m-80) cc_final: 0.5598 (m-10) REVERT: D 69 MET cc_start: 0.7400 (mtt) cc_final: 0.7065 (mtt) REVERT: D 281 GLU cc_start: 0.8169 (tp30) cc_final: 0.7733 (tp30) REVERT: D 282 ASN cc_start: 0.8155 (m-40) cc_final: 0.7846 (m110) REVERT: D 295 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6537 (ttt) REVERT: D 397 LYS cc_start: 0.7799 (ptpt) cc_final: 0.7497 (tmtt) REVERT: D 495 ASP cc_start: 0.8281 (m-30) cc_final: 0.7846 (m-30) REVERT: E 99 ARG cc_start: 0.7450 (mmm-85) cc_final: 0.6733 (mmm-85) REVERT: E 387 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6932 (mm110) REVERT: E 472 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8142 (mm-30) REVERT: E 495 ASP cc_start: 0.8066 (m-30) cc_final: 0.7608 (m-30) REVERT: E 533 ASP cc_start: 0.8494 (t0) cc_final: 0.8188 (t0) REVERT: F 207 MET cc_start: 0.8634 (mtm) cc_final: 0.8396 (mtm) REVERT: F 326 LYS cc_start: 0.7572 (ptmt) cc_final: 0.6909 (mtmt) REVERT: F 399 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7542 (mttt) REVERT: F 412 GLU cc_start: 0.7864 (pm20) cc_final: 0.7461 (tm-30) REVERT: F 533 ASP cc_start: 0.8650 (t0) cc_final: 0.8055 (t0) outliers start: 91 outliers final: 64 residues processed: 341 average time/residue: 0.3167 time to fit residues: 171.9745 Evaluate side-chains 338 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 151 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 243 optimal weight: 0.6980 chunk 272 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 282 ASN E 262 GLN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.179552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140476 restraints weight = 29503.110| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.12 r_work: 0.3482 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23231 Z= 0.124 Angle : 0.541 9.866 31413 Z= 0.280 Chirality : 0.043 0.208 3432 Planarity : 0.004 0.035 4121 Dihedral : 4.190 17.414 3228 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.11 % Allowed : 15.58 % Favored : 81.31 % 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: 1.41 (0.15), residues: 2952 helix: 2.37 (0.13), residues: 1524 sheet: -0.11 (0.26), residues: 378 loop : -0.84 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 338 HIS 0.003 0.001 HIS C 278 PHE 0.032 0.002 PHE F 304 TYR 0.012 0.001 TYR A 528 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 1416) hydrogen bonds : angle 3.99601 ( 4050) covalent geometry : bond 0.00288 (23231) covalent geometry : angle 0.54111 (31413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 290 time to evaluate : 2.422 Fit side-chains REVERT: A 67 PHE cc_start: 0.6000 (m-80) cc_final: 0.5527 (m-10) REVERT: A 69 MET cc_start: 0.7296 (mmt) cc_final: 0.6733 (mmt) REVERT: A 282 ASN cc_start: 0.8125 (m-40) cc_final: 0.7773 (m110) REVERT: A 326 LYS cc_start: 0.8337 (mttp) cc_final: 0.7720 (ptmt) REVERT: A 397 LYS cc_start: 0.7861 (ptpt) cc_final: 0.7575 (tmtt) REVERT: A 399 LYS cc_start: 0.7725 (mmmt) cc_final: 0.7339 (mttm) REVERT: A 495 ASP cc_start: 0.8148 (m-30) cc_final: 0.7729 (m-30) REVERT: B 319 TYR cc_start: 0.7912 (m-80) cc_final: 0.7562 (m-80) REVERT: B 326 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7289 (mtmt) REVERT: B 387 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7178 (mm110) REVERT: B 495 ASP cc_start: 0.8057 (m-30) cc_final: 0.7556 (m-30) REVERT: B 533 ASP cc_start: 0.8497 (t0) cc_final: 0.8226 (t0) REVERT: C 207 MET cc_start: 0.8570 (mtm) cc_final: 0.8330 (mtm) REVERT: C 387 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.7150 (mm110) REVERT: C 533 ASP cc_start: 0.8575 (t0) cc_final: 0.8102 (t0) REVERT: D 67 PHE cc_start: 0.6025 (m-80) cc_final: 0.5546 (m-10) REVERT: D 69 MET cc_start: 0.7297 (mtt) cc_final: 0.6916 (mtt) REVERT: D 281 GLU cc_start: 0.7887 (tp30) cc_final: 0.7546 (tp30) REVERT: D 282 ASN cc_start: 0.7980 (m-40) cc_final: 0.7614 (m110) REVERT: D 295 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6539 (ttt) REVERT: D 338 TRP cc_start: 0.7641 (t-100) cc_final: 0.7271 (t-100) REVERT: D 397 LYS cc_start: 0.7801 (ptpt) cc_final: 0.7495 (tmtt) REVERT: D 495 ASP cc_start: 0.8188 (m-30) cc_final: 0.7751 (m-30) REVERT: E 326 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7365 (mtmt) REVERT: E 387 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7122 (mm110) REVERT: E 495 ASP cc_start: 0.8001 (m-30) cc_final: 0.7569 (m-30) REVERT: E 533 ASP cc_start: 0.8469 (t0) cc_final: 0.8193 (t0) REVERT: F 207 MET cc_start: 0.8561 (mtm) cc_final: 0.8313 (mtm) REVERT: F 326 LYS cc_start: 0.7544 (ptmt) cc_final: 0.6898 (mtmt) REVERT: F 349 GLU cc_start: 0.7605 (pp20) cc_final: 0.6992 (pt0) REVERT: F 399 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7443 (mttt) REVERT: F 533 ASP cc_start: 0.8616 (t0) cc_final: 0.8134 (t0) outliers start: 74 outliers final: 62 residues processed: 329 average time/residue: 0.3149 time to fit residues: 166.6437 Evaluate side-chains 337 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 271 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 181 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 186 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN ** F 282 ASN ** 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 = 0.4083 r_free = 0.4083 target = 0.177538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138477 restraints weight = 29554.365| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.15 r_work: 0.3433 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23231 Z= 0.157 Angle : 0.566 9.587 31413 Z= 0.294 Chirality : 0.045 0.219 3432 Planarity : 0.004 0.036 4121 Dihedral : 4.234 17.638 3228 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.94 % Allowed : 15.37 % Favored : 81.69 % 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: 1.30 (0.15), residues: 2952 helix: 2.29 (0.13), residues: 1524 sheet: -0.05 (0.27), residues: 366 loop : -0.96 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 338 HIS 0.004 0.001 HIS A 142 PHE 0.031 0.002 PHE F 304 TYR 0.014 0.002 TYR F 170 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 1416) hydrogen bonds : angle 4.04385 ( 4050) covalent geometry : bond 0.00373 (23231) covalent geometry : angle 0.56604 (31413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 277 time to evaluate : 2.581 Fit side-chains REVERT: A 67 PHE cc_start: 0.5878 (m-80) cc_final: 0.5430 (m-10) REVERT: A 69 MET cc_start: 0.7241 (mmt) cc_final: 0.6665 (mmt) REVERT: A 282 ASN cc_start: 0.8041 (m-40) cc_final: 0.7661 (m110) REVERT: A 326 LYS cc_start: 0.8290 (mttp) cc_final: 0.7672 (ptmt) REVERT: A 397 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7587 (tmtt) REVERT: A 399 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7301 (mttm) REVERT: A 495 ASP cc_start: 0.8014 (m-30) cc_final: 0.7565 (m-30) REVERT: B 319 TYR cc_start: 0.7850 (m-80) cc_final: 0.7520 (m-80) REVERT: B 326 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7241 (mtmt) REVERT: B 387 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7182 (mm110) REVERT: B 495 ASP cc_start: 0.7817 (m-30) cc_final: 0.7307 (m-30) REVERT: B 533 ASP cc_start: 0.8328 (t0) cc_final: 0.8072 (t0) REVERT: C 207 MET cc_start: 0.8359 (mtm) cc_final: 0.8141 (mtm) REVERT: C 387 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7237 (mm110) REVERT: C 533 ASP cc_start: 0.8455 (t0) cc_final: 0.7914 (t0) REVERT: D 67 PHE cc_start: 0.5859 (m-80) cc_final: 0.5499 (m-10) REVERT: D 69 MET cc_start: 0.7163 (mtt) cc_final: 0.6761 (mtt) REVERT: D 282 ASN cc_start: 0.7936 (m-40) cc_final: 0.7544 (m110) REVERT: D 295 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6554 (ttt) REVERT: D 338 TRP cc_start: 0.7568 (t-100) cc_final: 0.7196 (t-100) REVERT: D 397 LYS cc_start: 0.7765 (ptpt) cc_final: 0.7512 (tmtt) REVERT: D 495 ASP cc_start: 0.8026 (m-30) cc_final: 0.7580 (m-30) REVERT: E 326 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7403 (mttt) REVERT: E 349 GLU cc_start: 0.7348 (pp20) cc_final: 0.6699 (pt0) REVERT: E 387 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7313 (mm110) REVERT: E 495 ASP cc_start: 0.7817 (m-30) cc_final: 0.7340 (m-30) REVERT: E 533 ASP cc_start: 0.8319 (t0) cc_final: 0.8067 (t0) REVERT: F 116 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8267 (tp) REVERT: F 207 MET cc_start: 0.8361 (mtm) cc_final: 0.8125 (mtm) REVERT: F 326 LYS cc_start: 0.7516 (ptmt) cc_final: 0.6895 (mtmt) REVERT: F 349 GLU cc_start: 0.7589 (pp20) cc_final: 0.7036 (pt0) REVERT: F 399 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7554 (mttt) REVERT: F 533 ASP cc_start: 0.8481 (t0) cc_final: 0.7936 (t0) outliers start: 70 outliers final: 62 residues processed: 313 average time/residue: 0.3108 time to fit residues: 158.2374 Evaluate side-chains 332 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 chunk 102 optimal weight: 0.2980 chunk 286 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN ** F 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141700 restraints weight = 29288.906| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.93 r_work: 0.3486 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23231 Z= 0.111 Angle : 0.526 9.445 31413 Z= 0.271 Chirality : 0.042 0.196 3432 Planarity : 0.004 0.040 4121 Dihedral : 4.076 17.064 3228 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.02 % Allowed : 15.29 % Favored : 81.69 % 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: 1.50 (0.15), residues: 2952 helix: 2.46 (0.13), residues: 1524 sheet: -0.08 (0.27), residues: 378 loop : -0.83 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 338 HIS 0.004 0.001 HIS B 448 PHE 0.032 0.002 PHE F 304 TYR 0.012 0.001 TYR A 528 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 1416) hydrogen bonds : angle 3.89350 ( 4050) covalent geometry : bond 0.00255 (23231) covalent geometry : angle 0.52628 (31413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12017.05 seconds wall clock time: 208 minutes 4.85 seconds (12484.85 seconds total)