Starting phenix.real_space_refine on Thu Mar 5 13:59:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s67_24852/03_2026/7s67_24852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s67_24852/03_2026/7s67_24852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s67_24852/03_2026/7s67_24852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s67_24852/03_2026/7s67_24852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s67_24852/03_2026/7s67_24852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s67_24852/03_2026/7s67_24852.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 90 5.16 5 C 14430 2.51 5 N 4056 2.21 5 O 4440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23058 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3783 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 469} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 92 Unusual residues: {' MG': 3, 'ADP': 1, 'ATP': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.70, per 1000 atoms: 0.20 Number of scatterers: 23058 At special positions: 0 Unit cell: (118.45, 118.45, 109.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 30 15.00 Mg 12 11.99 O 4440 8.00 N 4056 7.00 C 14430 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 41.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.968A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.619A pdb=" N GLU A 432 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 156 through 175 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 293 through 308 Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.638A pdb=" N ALA B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.968A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU B 432 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 156 through 175 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 293 through 308 Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.969A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU C 432 " --> pdb=" O HIS C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.607A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 Processing helix chain 'D' and resid 156 through 175 Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 293 through 308 Processing helix chain 'D' and resid 320 through 330 Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 385 removed outlier: 3.969A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU D 432 " --> pdb=" O HIS D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER E 124 " --> pdb=" O GLY E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 156 through 175 Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 293 through 308 Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 334 through 341 Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA E 354 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 379 through 385 removed outlier: 3.968A pdb=" N LEU E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU E 432 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER F 124 " --> pdb=" O GLY F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Processing helix chain 'F' and resid 156 through 175 Processing helix chain 'F' and resid 196 through 201 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 267 through 274 Processing helix chain 'F' and resid 293 through 308 Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.638A pdb=" N ALA F 354 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 379 through 385 removed outlier: 3.969A pdb=" N LEU F 383 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU F 432 " --> pdb=" O HIS F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN A 203 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA A 312 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL A 347 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 314 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 413 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 284 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN A 414 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 286 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER A 416 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 288 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 289 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR A 442 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET A 449 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE A 472 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU A 469 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 107 removed outlier: 4.077A pdb=" N ASN B 203 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 13.109A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA9, first strand: chain 'B' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA B 312 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 347 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 314 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 413 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 284 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN B 414 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 286 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER B 416 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY B 288 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 289 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 442 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET B 449 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE B 472 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU B 469 " --> pdb=" O LYS B 480 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN C 203 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AB5, first strand: chain 'C' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA C 312 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL C 347 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 314 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 413 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 284 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN C 414 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 286 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER C 416 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY C 288 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 289 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR C 442 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET C 449 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE C 472 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 469 " --> pdb=" O LYS C 480 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN D 203 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 262 through 263 Processing sheet with id=AC1, first strand: chain 'D' and resid 344 through 348 removed outlier: 6.931A pdb=" N ALA D 312 " --> pdb=" O LYS D 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL D 347 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D 314 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 413 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 284 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN D 414 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA D 286 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER D 416 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY D 288 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA D 289 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR D 442 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N MET D 449 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N ILE D 472 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU D 469 " --> pdb=" O LYS D 480 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'E' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN E 203 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 13.111A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 262 through 263 Processing sheet with id=AC6, first strand: chain 'E' and resid 344 through 348 removed outlier: 6.931A pdb=" N ALA E 312 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL E 347 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU E 314 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 413 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE E 284 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN E 414 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 286 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER E 416 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY E 288 " --> pdb=" O SER E 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 289 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR E 442 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET E 449 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N ILE E 472 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU E 469 " --> pdb=" O LYS E 480 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 486 through 487 Processing sheet with id=AC8, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC9, first strand: chain 'F' and resid 103 through 107 removed outlier: 4.077A pdb=" N ASN F 203 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 262 through 263 Processing sheet with id=AD2, first strand: chain 'F' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA F 312 " --> pdb=" O LYS F 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL F 347 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 314 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 413 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE F 284 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN F 414 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 286 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER F 416 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY F 288 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 289 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR F 442 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET F 449 " --> pdb=" O ILE F 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE F 472 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU F 469 " --> pdb=" O LYS F 480 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 486 through 487 1134 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.72 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4061 1.31 - 1.44: 5983 1.44 - 1.56: 13200 1.56 - 1.69: 42 1.69 - 1.81: 162 Bond restraints: 23448 Sorted by residual: bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C4 ADP D 603 " pdb=" C5 ADP D 603 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 ADP C 603 " pdb=" C5 ADP C 603 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 ADP A 603 " pdb=" C5 ADP A 603 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 23443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 31181 4.26 - 8.51: 469 8.51 - 12.77: 12 12.77 - 17.03: 0 17.03 - 21.28: 18 Bond angle restraints: 31680 Sorted by residual: angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 116.10 20.73 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 116.11 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 116.11 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 ... (remaining 31675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 13864 29.18 - 58.36: 272 58.36 - 87.54: 42 87.54 - 116.72: 6 116.72 - 145.90: 6 Dihedral angle restraints: 14190 sinusoidal: 5928 harmonic: 8262 Sorted by residual: dihedral pdb=" C5' ADP B 603 " pdb=" O5' ADP B 603 " pdb=" PA ADP B 603 " pdb=" O2A ADP B 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.10 145.90 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual 300.00 154.15 145.85 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP A 603 " pdb=" O5' ADP A 603 " pdb=" PA ADP A 603 " pdb=" O2A ADP A 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.15 145.85 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 14187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2513 0.064 - 0.128: 813 0.128 - 0.191: 176 0.191 - 0.255: 20 0.255 - 0.319: 12 Chirality restraints: 3534 Sorted by residual: chirality pdb=" CA HIS D 429 " pdb=" N HIS D 429 " pdb=" C HIS D 429 " pdb=" CB HIS D 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA HIS A 429 " pdb=" N HIS A 429 " pdb=" C HIS A 429 " pdb=" CB HIS A 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA HIS E 429 " pdb=" N HIS E 429 " pdb=" C HIS E 429 " pdb=" CB HIS E 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 3531 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP C 603 " -0.175 2.00e-02 2.50e+03 7.17e-02 1.41e+02 pdb=" C2 ADP C 603 " 0.024 2.00e-02 2.50e+03 pdb=" C4 ADP C 603 " 0.065 2.00e-02 2.50e+03 pdb=" C5 ADP C 603 " 0.028 2.00e-02 2.50e+03 pdb=" C6 ADP C 603 " -0.016 2.00e-02 2.50e+03 pdb=" C8 ADP C 603 " 0.066 2.00e-02 2.50e+03 pdb=" N1 ADP C 603 " -0.029 2.00e-02 2.50e+03 pdb=" N3 ADP C 603 " 0.063 2.00e-02 2.50e+03 pdb=" N6 ADP C 603 " -0.092 2.00e-02 2.50e+03 pdb=" N7 ADP C 603 " 0.023 2.00e-02 2.50e+03 pdb=" N9 ADP C 603 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 902 " 0.175 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" C2 ADP E 902 " -0.024 2.00e-02 2.50e+03 pdb=" C4 ADP E 902 " -0.065 2.00e-02 2.50e+03 pdb=" C5 ADP E 902 " -0.028 2.00e-02 2.50e+03 pdb=" C6 ADP E 902 " 0.016 2.00e-02 2.50e+03 pdb=" C8 ADP E 902 " -0.066 2.00e-02 2.50e+03 pdb=" N1 ADP E 902 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ADP E 902 " -0.063 2.00e-02 2.50e+03 pdb=" N6 ADP E 902 " 0.092 2.00e-02 2.50e+03 pdb=" N7 ADP E 902 " -0.023 2.00e-02 2.50e+03 pdb=" N9 ADP E 902 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 603 " -0.175 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" C2 ADP B 603 " 0.024 2.00e-02 2.50e+03 pdb=" C4 ADP B 603 " 0.064 2.00e-02 2.50e+03 pdb=" C5 ADP B 603 " 0.028 2.00e-02 2.50e+03 pdb=" C6 ADP B 603 " -0.016 2.00e-02 2.50e+03 pdb=" C8 ADP B 603 " 0.066 2.00e-02 2.50e+03 pdb=" N1 ADP B 603 " -0.029 2.00e-02 2.50e+03 pdb=" N3 ADP B 603 " 0.063 2.00e-02 2.50e+03 pdb=" N6 ADP B 603 " -0.092 2.00e-02 2.50e+03 pdb=" N7 ADP B 603 " 0.023 2.00e-02 2.50e+03 pdb=" N9 ADP B 603 " 0.043 2.00e-02 2.50e+03 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 64 2.43 - 3.05: 15207 3.05 - 3.67: 34459 3.67 - 4.28: 56802 4.28 - 4.90: 89877 Nonbonded interactions: 196409 Sorted by model distance: nonbonded pdb=" NH1 ARG F 226 " pdb=" O2G ATP F 601 " model vdw 1.815 3.120 nonbonded pdb=" NH1 ARG C 226 " pdb=" O2G ATP B 601 " model vdw 1.887 3.120 nonbonded pdb=" NH1 ARG E 226 " pdb=" O2G ATP D 601 " model vdw 1.912 3.120 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.917 2.170 nonbonded pdb=" O2G ATP A 605 " pdb="MG MG A 606 " model vdw 1.918 2.170 ... (remaining 196404 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 16 through 497) selection = (chain 'B' and resid 16 through 497) selection = (chain 'C' and resid 16 through 497) selection = (chain 'D' and resid 16 through 497) selection = (chain 'E' and resid 16 through 497) selection = (chain 'F' and resid 16 through 497) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.450 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 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 : 0.015 0.516 23454 Z= 1.030 Angle : 1.395 21.283 31680 Z= 0.953 Chirality : 0.067 0.319 3534 Planarity : 0.011 0.072 4062 Dihedral : 12.758 145.899 8886 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2880 helix: -0.43 (0.13), residues: 1038 sheet: 0.76 (0.21), residues: 696 loop : 0.65 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 451 TYR 0.109 0.015 TYR D 442 PHE 0.037 0.008 PHE E 237 TRP 0.066 0.018 TRP E 92 HIS 0.009 0.003 HIS F 423 Details of bonding type rmsd covalent geometry : bond 0.01306 (23448) covalent geometry : angle 1.39476 (31680) hydrogen bonds : bond 0.16785 ( 1134) hydrogen bonds : angle 7.08064 ( 3060) Misc. bond : bond 0.46646 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1032 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.7257 (m-30) cc_final: 0.6777 (m-30) REVERT: A 234 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 235 TYR cc_start: 0.8591 (m-80) cc_final: 0.8122 (m-80) REVERT: A 247 PHE cc_start: 0.8559 (m-80) cc_final: 0.8329 (m-10) REVERT: A 442 TYR cc_start: 0.6837 (m-80) cc_final: 0.6580 (m-80) REVERT: B 82 ASP cc_start: 0.7607 (m-30) cc_final: 0.7200 (m-30) REVERT: B 234 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7492 (mt-10) REVERT: B 235 TYR cc_start: 0.8637 (m-80) cc_final: 0.8243 (m-80) REVERT: B 247 PHE cc_start: 0.8546 (m-80) cc_final: 0.8273 (m-10) REVERT: B 357 GLU cc_start: 0.8395 (mp0) cc_final: 0.8015 (mp0) REVERT: C 82 ASP cc_start: 0.7449 (m-30) cc_final: 0.7186 (m-30) REVERT: C 247 PHE cc_start: 0.8547 (m-80) cc_final: 0.8334 (m-10) REVERT: C 357 GLU cc_start: 0.8516 (mp0) cc_final: 0.8191 (mp0) REVERT: D 235 TYR cc_start: 0.8608 (m-80) cc_final: 0.8276 (m-80) REVERT: D 357 GLU cc_start: 0.8587 (mp0) cc_final: 0.8247 (mp0) REVERT: D 442 TYR cc_start: 0.6727 (m-80) cc_final: 0.6517 (m-80) REVERT: E 82 ASP cc_start: 0.7681 (m-30) cc_final: 0.7254 (m-30) REVERT: E 188 TYR cc_start: 0.8332 (m-80) cc_final: 0.8129 (m-80) REVERT: E 234 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7535 (mt-10) REVERT: E 235 TYR cc_start: 0.8673 (m-80) cc_final: 0.8273 (m-80) REVERT: E 247 PHE cc_start: 0.8608 (m-80) cc_final: 0.8218 (m-10) REVERT: E 357 GLU cc_start: 0.8517 (mp0) cc_final: 0.8193 (mp0) REVERT: F 82 ASP cc_start: 0.7450 (m-30) cc_final: 0.7063 (m-30) REVERT: F 234 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7924 (mt-10) REVERT: F 247 PHE cc_start: 0.8587 (m-80) cc_final: 0.8319 (m-10) REVERT: F 357 GLU cc_start: 0.8448 (mp0) cc_final: 0.8141 (mp0) outliers start: 0 outliers final: 0 residues processed: 1032 average time/residue: 0.1902 time to fit residues: 286.7780 Evaluate side-chains 576 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 304 ASN A 327 ASN A 341 GLN A 368 ASN B 245 ASN B 260 ASN B 341 GLN B 342 ASN ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN C 341 GLN C 342 ASN C 368 ASN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS D 260 ASN D 304 ASN D 368 ASN D 463 HIS E 245 ASN E 260 ASN E 304 ASN E 341 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN F 341 GLN F 342 ASN F 368 ASN ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131561 restraints weight = 37196.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135955 restraints weight = 20116.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.138911 restraints weight = 13213.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140982 restraints weight = 9873.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142269 restraints weight = 7985.961| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23454 Z= 0.173 Angle : 0.664 7.006 31680 Z= 0.351 Chirality : 0.047 0.174 3534 Planarity : 0.005 0.047 4062 Dihedral : 11.978 123.782 3456 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.30 % Allowed : 12.10 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 2880 helix: 0.59 (0.15), residues: 1050 sheet: 0.44 (0.20), residues: 714 loop : 0.34 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 161 TYR 0.022 0.002 TYR C 442 PHE 0.022 0.002 PHE A 419 TRP 0.018 0.002 TRP F 331 HIS 0.019 0.003 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00398 (23448) covalent geometry : angle 0.66435 (31680) hydrogen bonds : bond 0.04363 ( 1134) hydrogen bonds : angle 5.05744 ( 3060) Misc. bond : bond 0.00097 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 666 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7435 (mmt) cc_final: 0.7181 (mmt) REVERT: A 234 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8375 (mt-10) REVERT: A 235 TYR cc_start: 0.8832 (m-80) cc_final: 0.8452 (m-80) REVERT: A 269 ARG cc_start: 0.6530 (mtp85) cc_final: 0.5856 (ttm110) REVERT: A 393 ARG cc_start: 0.7906 (ptt-90) cc_final: 0.7627 (ptt-90) REVERT: A 420 MET cc_start: 0.5924 (tpp) cc_final: 0.5034 (tpp) REVERT: A 454 ASN cc_start: 0.8072 (t0) cc_final: 0.7709 (t0) REVERT: A 459 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6828 (mtm-85) REVERT: B 132 TYR cc_start: 0.7168 (t80) cc_final: 0.6756 (t80) REVERT: B 234 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8131 (mt-10) REVERT: B 235 TYR cc_start: 0.8810 (m-80) cc_final: 0.8495 (m-80) REVERT: B 393 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7652 (ptt-90) REVERT: B 394 GLN cc_start: 0.8639 (mt0) cc_final: 0.7855 (mp10) REVERT: C 166 ARG cc_start: 0.8249 (mtt180) cc_final: 0.8029 (mtt180) REVERT: C 216 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8426 (mmt90) REVERT: C 273 MET cc_start: 0.7605 (mtp) cc_final: 0.7317 (mtp) REVERT: C 304 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7976 (t0) REVERT: C 420 MET cc_start: 0.5753 (tpp) cc_final: 0.5050 (tpp) REVERT: D 162 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7842 (mmm160) REVERT: D 234 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8208 (mt-10) REVERT: D 235 TYR cc_start: 0.8864 (m-80) cc_final: 0.8510 (m-80) REVERT: D 338 MET cc_start: 0.7940 (mmt) cc_final: 0.7379 (mmt) REVERT: D 393 ARG cc_start: 0.7945 (ptt-90) cc_final: 0.7671 (ptt-90) REVERT: D 420 MET cc_start: 0.5876 (tpp) cc_final: 0.5462 (tpp) REVERT: D 457 LYS cc_start: 0.9029 (ptmm) cc_final: 0.8744 (pttp) REVERT: D 459 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6968 (mtm-85) REVERT: D 469 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6937 (tm-30) REVERT: E 132 TYR cc_start: 0.7256 (t80) cc_final: 0.6920 (t80) REVERT: E 166 ARG cc_start: 0.7622 (mtm180) cc_final: 0.7392 (mtm180) REVERT: E 234 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8104 (mt-10) REVERT: E 235 TYR cc_start: 0.8784 (m-80) cc_final: 0.8521 (m-80) REVERT: E 245 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.8054 (m-40) REVERT: E 274 CYS cc_start: 0.8344 (m) cc_final: 0.8056 (t) REVERT: E 393 ARG cc_start: 0.7881 (ptt-90) cc_final: 0.7624 (ptt-90) REVERT: E 394 GLN cc_start: 0.8395 (mt0) cc_final: 0.7685 (mp10) REVERT: E 432 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8148 (mm-30) REVERT: E 461 SER cc_start: 0.8059 (t) cc_final: 0.7848 (t) REVERT: F 82 ASP cc_start: 0.7993 (m-30) cc_final: 0.7772 (m-30) REVERT: F 86 ASN cc_start: 0.8709 (m-40) cc_final: 0.8435 (m-40) REVERT: F 216 ARG cc_start: 0.8749 (mmt180) cc_final: 0.8403 (mmt90) REVERT: F 272 GLU cc_start: 0.8193 (pt0) cc_final: 0.7938 (mm-30) REVERT: F 273 MET cc_start: 0.7490 (mtp) cc_final: 0.7155 (mtp) REVERT: F 442 TYR cc_start: 0.7632 (m-80) cc_final: 0.7281 (m-80) REVERT: F 457 LYS cc_start: 0.8574 (pttp) cc_final: 0.8331 (pttp) outliers start: 56 outliers final: 40 residues processed: 699 average time/residue: 0.1619 time to fit residues: 174.6457 Evaluate side-chains 600 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 558 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 178 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN C 429 HIS C 463 HIS D 429 HIS D 463 HIS E 304 ASN E 308 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS F 463 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119609 restraints weight = 38501.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123567 restraints weight = 21309.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126237 restraints weight = 14248.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127855 restraints weight = 10795.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129100 restraints weight = 8982.540| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23454 Z= 0.262 Angle : 0.697 10.698 31680 Z= 0.360 Chirality : 0.048 0.158 3534 Planarity : 0.005 0.045 4062 Dihedral : 12.004 114.213 3456 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.58 % Allowed : 13.87 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 2880 helix: 0.73 (0.16), residues: 1050 sheet: -0.12 (0.19), residues: 780 loop : 0.09 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 162 TYR 0.028 0.002 TYR A 402 PHE 0.025 0.002 PHE E 392 TRP 0.036 0.003 TRP C 331 HIS 0.018 0.003 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00603 (23448) covalent geometry : angle 0.69677 (31680) hydrogen bonds : bond 0.03946 ( 1134) hydrogen bonds : angle 4.99687 ( 3060) Misc. bond : bond 0.00043 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 585 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TYR cc_start: 0.7403 (m-80) cc_final: 0.6964 (m-80) REVERT: A 203 ASN cc_start: 0.8772 (m-40) cc_final: 0.8329 (m110) REVERT: A 235 TYR cc_start: 0.8898 (m-80) cc_final: 0.8411 (m-80) REVERT: A 269 ARG cc_start: 0.6745 (mtp85) cc_final: 0.6144 (ttm110) REVERT: A 274 CYS cc_start: 0.8362 (m) cc_final: 0.7906 (t) REVERT: A 338 MET cc_start: 0.7991 (mmt) cc_final: 0.7481 (mmt) REVERT: A 372 PRO cc_start: 0.9066 (Cg_endo) cc_final: 0.8862 (Cg_exo) REVERT: A 392 PHE cc_start: 0.8816 (t80) cc_final: 0.8590 (t80) REVERT: A 420 MET cc_start: 0.6315 (tpp) cc_final: 0.5408 (tpp) REVERT: A 469 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6731 (tm-30) REVERT: B 194 TYR cc_start: 0.7348 (m-80) cc_final: 0.6833 (m-80) REVERT: B 221 GLU cc_start: 0.7946 (tt0) cc_final: 0.7734 (tt0) REVERT: B 234 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7960 (mt-10) REVERT: B 393 ARG cc_start: 0.7963 (ptt-90) cc_final: 0.7729 (ptt-90) REVERT: B 394 GLN cc_start: 0.8606 (mt0) cc_final: 0.7897 (mp10) REVERT: B 469 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 191 ILE cc_start: 0.8224 (mp) cc_final: 0.7702 (mt) REVERT: C 194 TYR cc_start: 0.7583 (m-80) cc_final: 0.7038 (m-80) REVERT: C 203 ASN cc_start: 0.8705 (m-40) cc_final: 0.8129 (m-40) REVERT: C 216 ARG cc_start: 0.8785 (mmt180) cc_final: 0.8469 (mmt90) REVERT: D 194 TYR cc_start: 0.7348 (m-80) cc_final: 0.6996 (m-80) REVERT: D 235 TYR cc_start: 0.8880 (m-80) cc_final: 0.8550 (m-80) REVERT: D 274 CYS cc_start: 0.8551 (m) cc_final: 0.7738 (t) REVERT: D 392 PHE cc_start: 0.8828 (t80) cc_final: 0.8623 (t80) REVERT: D 457 LYS cc_start: 0.9096 (ptmm) cc_final: 0.8824 (pttp) REVERT: E 194 TYR cc_start: 0.7273 (m-80) cc_final: 0.6840 (m-80) REVERT: E 221 GLU cc_start: 0.7975 (tt0) cc_final: 0.7729 (tt0) REVERT: E 234 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7967 (mt-10) REVERT: E 245 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8008 (t0) REVERT: E 345 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8488 (mtpp) REVERT: E 394 GLN cc_start: 0.8359 (mt0) cc_final: 0.7852 (mp10) REVERT: E 420 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.5994 (tpp) REVERT: F 194 TYR cc_start: 0.7553 (m-80) cc_final: 0.7092 (m-80) REVERT: F 216 ARG cc_start: 0.8745 (mmt180) cc_final: 0.8424 (mtt-85) REVERT: F 457 LYS cc_start: 0.8942 (pttp) cc_final: 0.8658 (pttp) REVERT: F 469 GLU cc_start: 0.7454 (tt0) cc_final: 0.7098 (tm-30) outliers start: 87 outliers final: 74 residues processed: 627 average time/residue: 0.1559 time to fit residues: 152.6229 Evaluate side-chains 602 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 526 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 429 HIS Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 429 HIS Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 200 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN C 327 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 304 ASN ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121589 restraints weight = 38350.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125587 restraints weight = 21112.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128334 restraints weight = 14133.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130133 restraints weight = 10682.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131335 restraints weight = 8834.787| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23454 Z= 0.151 Angle : 0.616 7.795 31680 Z= 0.315 Chirality : 0.045 0.152 3534 Planarity : 0.004 0.043 4062 Dihedral : 11.590 112.733 3456 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.25 % Allowed : 15.56 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2880 helix: 0.95 (0.16), residues: 1050 sheet: -0.09 (0.19), residues: 786 loop : 0.04 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 162 TYR 0.031 0.002 TYR F 402 PHE 0.017 0.002 PHE D 59 TRP 0.017 0.002 TRP C 331 HIS 0.022 0.003 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00344 (23448) covalent geometry : angle 0.61583 (31680) hydrogen bonds : bond 0.03383 ( 1134) hydrogen bonds : angle 4.69966 ( 3060) Misc. bond : bond 0.00050 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 594 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TYR cc_start: 0.7439 (m-80) cc_final: 0.6982 (m-80) REVERT: A 235 TYR cc_start: 0.8760 (m-80) cc_final: 0.8281 (m-80) REVERT: A 247 PHE cc_start: 0.8853 (m-80) cc_final: 0.8522 (m-10) REVERT: A 269 ARG cc_start: 0.6795 (mtp85) cc_final: 0.6302 (ttm170) REVERT: A 372 PRO cc_start: 0.9054 (Cg_endo) cc_final: 0.8842 (Cg_exo) REVERT: A 385 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7550 (ttm170) REVERT: A 393 ARG cc_start: 0.8033 (ptt-90) cc_final: 0.7727 (ptt-90) REVERT: A 420 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5450 (tpp) REVERT: A 469 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 194 TYR cc_start: 0.7303 (m-80) cc_final: 0.6887 (m-80) REVERT: B 217 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7894 (ttt-90) REVERT: B 221 GLU cc_start: 0.7928 (tt0) cc_final: 0.7680 (tt0) REVERT: B 234 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 392 PHE cc_start: 0.8679 (t80) cc_final: 0.8455 (t80) REVERT: B 394 GLN cc_start: 0.8656 (mt0) cc_final: 0.7889 (mp10) REVERT: B 420 MET cc_start: 0.5964 (OUTLIER) cc_final: 0.5619 (tpp) REVERT: B 423 HIS cc_start: 0.5492 (t-90) cc_final: 0.5120 (t70) REVERT: C 194 TYR cc_start: 0.7477 (m-80) cc_final: 0.7044 (m-80) REVERT: C 216 ARG cc_start: 0.8819 (mmt180) cc_final: 0.8600 (mmt90) REVERT: C 234 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8270 (mt-10) REVERT: D 162 ARG cc_start: 0.8400 (mmm160) cc_final: 0.7974 (tpt170) REVERT: D 166 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7255 (mtt180) REVERT: D 194 TYR cc_start: 0.7452 (m-80) cc_final: 0.7124 (m-80) REVERT: D 235 TYR cc_start: 0.8799 (m-80) cc_final: 0.8437 (m-80) REVERT: D 385 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7523 (ttm170) REVERT: D 393 ARG cc_start: 0.8012 (ptt-90) cc_final: 0.7711 (ptt-90) REVERT: D 457 LYS cc_start: 0.8981 (ptmm) cc_final: 0.8701 (pttp) REVERT: E 194 TYR cc_start: 0.7290 (m-80) cc_final: 0.6861 (m-80) REVERT: E 234 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8090 (mt-10) REVERT: E 304 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8422 (t0) REVERT: E 394 GLN cc_start: 0.8628 (mt0) cc_final: 0.7904 (mp10) REVERT: E 432 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8232 (mm-30) REVERT: E 458 MET cc_start: 0.6688 (tmm) cc_final: 0.6427 (tmm) REVERT: E 461 SER cc_start: 0.8582 (t) cc_final: 0.8122 (t) REVERT: F 191 ILE cc_start: 0.7966 (mp) cc_final: 0.7537 (mt) REVERT: F 194 TYR cc_start: 0.7562 (m-80) cc_final: 0.7169 (m-80) REVERT: F 216 ARG cc_start: 0.8742 (mmt180) cc_final: 0.8518 (mtt-85) REVERT: F 234 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8078 (mt-10) REVERT: F 315 PHE cc_start: 0.8912 (m-10) cc_final: 0.8674 (m-10) REVERT: F 457 LYS cc_start: 0.9001 (pttp) cc_final: 0.8682 (pttp) REVERT: F 458 MET cc_start: 0.6950 (tmm) cc_final: 0.6637 (tmm) outliers start: 79 outliers final: 62 residues processed: 638 average time/residue: 0.1525 time to fit residues: 153.6779 Evaluate side-chains 599 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 534 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 202 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 68 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 ASN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121108 restraints weight = 38339.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125013 restraints weight = 21154.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127680 restraints weight = 14140.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129452 restraints weight = 10728.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130520 restraints weight = 8861.261| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23454 Z= 0.166 Angle : 0.612 8.312 31680 Z= 0.312 Chirality : 0.045 0.153 3534 Planarity : 0.004 0.044 4062 Dihedral : 11.137 113.245 3456 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.50 % Allowed : 16.91 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2880 helix: 1.11 (0.16), residues: 1050 sheet: -0.13 (0.20), residues: 720 loop : 0.05 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.029 0.002 TYR F 402 PHE 0.017 0.002 PHE A 59 TRP 0.012 0.001 TRP C 331 HIS 0.016 0.003 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00383 (23448) covalent geometry : angle 0.61158 (31680) hydrogen bonds : bond 0.03250 ( 1134) hydrogen bonds : angle 4.65462 ( 3060) Misc. bond : bond 0.00037 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 574 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TYR cc_start: 0.7497 (m-80) cc_final: 0.7050 (m-80) REVERT: A 235 TYR cc_start: 0.8780 (m-80) cc_final: 0.8288 (m-80) REVERT: A 255 THR cc_start: 0.8233 (t) cc_final: 0.8009 (t) REVERT: A 269 ARG cc_start: 0.6852 (mtp85) cc_final: 0.6486 (ttm170) REVERT: A 361 GLN cc_start: 0.8997 (tp40) cc_final: 0.8767 (tp40) REVERT: A 393 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7775 (ptt-90) REVERT: A 420 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5643 (tpp) REVERT: A 442 TYR cc_start: 0.8000 (m-80) cc_final: 0.7276 (m-80) REVERT: A 457 LYS cc_start: 0.8725 (pttp) cc_final: 0.8487 (pttp) REVERT: A 469 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6793 (tm-30) REVERT: B 194 TYR cc_start: 0.7432 (m-80) cc_final: 0.6996 (m-80) REVERT: B 221 GLU cc_start: 0.7963 (tt0) cc_final: 0.7707 (tt0) REVERT: B 234 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8001 (mt-10) REVERT: B 394 GLN cc_start: 0.8573 (mt0) cc_final: 0.7903 (mp10) REVERT: B 420 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5640 (tpp) REVERT: C 185 ILE cc_start: 0.9149 (mt) cc_final: 0.8875 (mm) REVERT: C 194 TYR cc_start: 0.7594 (m-80) cc_final: 0.7180 (m-80) REVERT: C 216 ARG cc_start: 0.8812 (mmt180) cc_final: 0.8606 (mmt90) REVERT: C 234 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8272 (mt-10) REVERT: D 162 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8078 (tpt170) REVERT: D 166 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7271 (mtt180) REVERT: D 194 TYR cc_start: 0.7545 (m-80) cc_final: 0.7206 (m-80) REVERT: D 235 TYR cc_start: 0.8791 (m-80) cc_final: 0.8397 (m-80) REVERT: D 247 PHE cc_start: 0.8687 (m-80) cc_final: 0.8388 (m-10) REVERT: D 393 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7743 (ptt-90) REVERT: D 420 MET cc_start: 0.6749 (tpp) cc_final: 0.6491 (tpp) REVERT: D 457 LYS cc_start: 0.9035 (ptmm) cc_final: 0.8802 (pttp) REVERT: D 469 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7202 (tm-30) REVERT: E 194 TYR cc_start: 0.7408 (m-80) cc_final: 0.6990 (m-80) REVERT: E 203 ASN cc_start: 0.8724 (m-40) cc_final: 0.8191 (m110) REVERT: E 234 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7992 (mt-10) REVERT: E 394 GLN cc_start: 0.8508 (mt0) cc_final: 0.7926 (mp10) REVERT: E 420 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5576 (tpp) REVERT: E 432 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8171 (mm-30) REVERT: E 458 MET cc_start: 0.6792 (tmm) cc_final: 0.6359 (tmm) REVERT: E 461 SER cc_start: 0.8408 (t) cc_final: 0.7948 (t) REVERT: F 194 TYR cc_start: 0.7526 (m-80) cc_final: 0.7159 (m-80) REVERT: F 234 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8074 (mt-10) REVERT: F 372 PRO cc_start: 0.9196 (Cg_endo) cc_final: 0.8902 (Cg_exo) REVERT: F 435 ASP cc_start: 0.7730 (t0) cc_final: 0.6776 (t0) REVERT: F 450 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7842 (p) REVERT: F 457 LYS cc_start: 0.8927 (pttp) cc_final: 0.8686 (pttp) REVERT: F 458 MET cc_start: 0.7133 (tmm) cc_final: 0.6655 (tmm) outliers start: 85 outliers final: 66 residues processed: 618 average time/residue: 0.1555 time to fit residues: 150.4642 Evaluate side-chains 612 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 540 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 29 optimal weight: 10.0000 chunk 127 optimal weight: 0.4980 chunk 216 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN A 429 HIS ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 308 ASN F 131 ASN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116004 restraints weight = 39241.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119696 restraints weight = 22120.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122244 restraints weight = 15091.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123936 restraints weight = 11628.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.125022 restraints weight = 9732.080| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23454 Z= 0.275 Angle : 0.704 14.901 31680 Z= 0.358 Chirality : 0.047 0.156 3534 Planarity : 0.005 0.046 4062 Dihedral : 10.857 111.078 3456 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.24 % Allowed : 17.82 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2880 helix: 0.96 (0.16), residues: 1050 sheet: -0.32 (0.19), residues: 720 loop : -0.24 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 184 TYR 0.037 0.002 TYR C 402 PHE 0.027 0.003 PHE B 392 TRP 0.017 0.002 TRP C 331 HIS 0.017 0.003 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00639 (23448) covalent geometry : angle 0.70414 (31680) hydrogen bonds : bond 0.03620 ( 1134) hydrogen bonds : angle 4.89958 ( 3060) Misc. bond : bond 0.00014 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 568 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8789 (m-80) cc_final: 0.8244 (m-80) REVERT: A 247 PHE cc_start: 0.8711 (m-80) cc_final: 0.8450 (m-10) REVERT: A 393 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7758 (ptt-90) REVERT: A 420 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5843 (tpp) REVERT: A 457 LYS cc_start: 0.8808 (pttp) cc_final: 0.8606 (pttp) REVERT: A 469 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6908 (tm-30) REVERT: B 170 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7511 (mtm180) REVERT: B 234 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 394 GLN cc_start: 0.8599 (mt0) cc_final: 0.7933 (mp10) REVERT: B 402 TYR cc_start: 0.8705 (t80) cc_final: 0.8273 (t80) REVERT: B 420 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5643 (tpp) REVERT: C 170 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7902 (mtm-85) REVERT: C 194 TYR cc_start: 0.7574 (m-80) cc_final: 0.7196 (m-80) REVERT: C 216 ARG cc_start: 0.8839 (mmt180) cc_final: 0.8565 (mmt90) REVERT: C 234 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8207 (mt-10) REVERT: C 247 PHE cc_start: 0.8596 (m-80) cc_final: 0.8048 (m-10) REVERT: C 457 LYS cc_start: 0.8887 (pttp) cc_final: 0.8590 (pttp) REVERT: D 86 ASN cc_start: 0.8522 (m-40) cc_final: 0.8320 (m-40) REVERT: D 162 ARG cc_start: 0.8413 (mmm160) cc_final: 0.8131 (tpt170) REVERT: D 166 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7268 (mtt180) REVERT: D 194 TYR cc_start: 0.7694 (m-80) cc_final: 0.7327 (m-80) REVERT: D 235 TYR cc_start: 0.8795 (m-80) cc_final: 0.8437 (m-80) REVERT: D 393 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7778 (ptt-90) REVERT: D 442 TYR cc_start: 0.7768 (m-10) cc_final: 0.7546 (m-10) REVERT: D 457 LYS cc_start: 0.9110 (ptmm) cc_final: 0.8889 (pttp) REVERT: D 469 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7342 (tm-30) REVERT: E 170 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7594 (mtm180) REVERT: E 234 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7861 (mt-10) REVERT: E 304 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8678 (t0) REVERT: E 345 LYS cc_start: 0.8732 (mtpp) cc_final: 0.7821 (ttpt) REVERT: E 394 GLN cc_start: 0.8568 (mt0) cc_final: 0.8007 (mp10) REVERT: E 432 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 456 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8170 (t80) REVERT: E 458 MET cc_start: 0.6988 (tmm) cc_final: 0.6587 (tmm) REVERT: E 461 SER cc_start: 0.8472 (t) cc_final: 0.8235 (t) REVERT: F 166 ARG cc_start: 0.8273 (mtt90) cc_final: 0.8032 (mmt90) REVERT: F 194 TYR cc_start: 0.7609 (m-80) cc_final: 0.7229 (m-80) REVERT: F 234 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8076 (mt-10) REVERT: F 247 PHE cc_start: 0.8614 (m-80) cc_final: 0.8071 (m-10) REVERT: F 372 PRO cc_start: 0.9215 (Cg_endo) cc_final: 0.8959 (Cg_exo) REVERT: F 458 MET cc_start: 0.7226 (tmm) cc_final: 0.6776 (tmm) outliers start: 103 outliers final: 83 residues processed: 618 average time/residue: 0.1478 time to fit residues: 144.6213 Evaluate side-chains 623 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 534 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 126 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 308 ASN ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119165 restraints weight = 38559.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122963 restraints weight = 21687.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125542 restraints weight = 14711.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127235 restraints weight = 11299.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128375 restraints weight = 9441.362| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23454 Z= 0.155 Angle : 0.634 9.952 31680 Z= 0.320 Chirality : 0.045 0.172 3534 Planarity : 0.004 0.043 4062 Dihedral : 10.378 112.951 3456 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.29 % Allowed : 19.47 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2880 helix: 1.12 (0.16), residues: 1050 sheet: -0.18 (0.20), residues: 696 loop : -0.22 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 385 TYR 0.035 0.002 TYR C 402 PHE 0.018 0.002 PHE E 59 TRP 0.013 0.002 TRP C 331 HIS 0.023 0.003 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00356 (23448) covalent geometry : angle 0.63375 (31680) hydrogen bonds : bond 0.03173 ( 1134) hydrogen bonds : angle 4.67492 ( 3060) Misc. bond : bond 0.00037 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 590 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8788 (mmt180) cc_final: 0.8455 (mmt90) REVERT: A 235 TYR cc_start: 0.8723 (m-80) cc_final: 0.8173 (m-80) REVERT: A 247 PHE cc_start: 0.8778 (m-80) cc_final: 0.8530 (m-10) REVERT: A 420 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5684 (tpp) REVERT: A 457 LYS cc_start: 0.8758 (pttp) cc_final: 0.8555 (pttp) REVERT: A 469 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6807 (tm-30) REVERT: B 166 ARG cc_start: 0.8022 (ptp-170) cc_final: 0.7751 (ptp-170) REVERT: B 170 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7489 (mtm180) REVERT: B 216 ARG cc_start: 0.8865 (mmt180) cc_final: 0.8504 (mmt90) REVERT: B 234 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 394 GLN cc_start: 0.8384 (mt0) cc_final: 0.7756 (mp10) REVERT: B 402 TYR cc_start: 0.8814 (t80) cc_final: 0.8381 (t80) REVERT: C 187 GLU cc_start: 0.6845 (mp0) cc_final: 0.6432 (mp0) REVERT: C 194 TYR cc_start: 0.7572 (m-80) cc_final: 0.7244 (m-80) REVERT: C 234 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 247 PHE cc_start: 0.8695 (m-80) cc_final: 0.8314 (m-10) REVERT: C 361 GLN cc_start: 0.9130 (tp40) cc_final: 0.8900 (tp40) REVERT: C 372 PRO cc_start: 0.9178 (Cg_endo) cc_final: 0.8899 (Cg_exo) REVERT: C 457 LYS cc_start: 0.8849 (pttp) cc_final: 0.8628 (pttp) REVERT: D 162 ARG cc_start: 0.8363 (mmm160) cc_final: 0.8022 (tpt170) REVERT: D 166 ARG cc_start: 0.7893 (mtm180) cc_final: 0.7225 (mtt180) REVERT: D 194 TYR cc_start: 0.7607 (m-80) cc_final: 0.7272 (m-80) REVERT: D 235 TYR cc_start: 0.8755 (m-80) cc_final: 0.8394 (m-80) REVERT: D 247 PHE cc_start: 0.8692 (m-80) cc_final: 0.8485 (m-10) REVERT: D 374 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8356 (mtp180) REVERT: D 393 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7785 (ptt-90) REVERT: D 469 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7324 (tm-30) REVERT: E 170 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7637 (mtm180) REVERT: E 216 ARG cc_start: 0.8914 (mmt180) cc_final: 0.8590 (mmt90) REVERT: E 234 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7911 (mt-10) REVERT: E 304 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8609 (t0) REVERT: E 394 GLN cc_start: 0.8576 (mt0) cc_final: 0.8021 (mp10) REVERT: E 458 MET cc_start: 0.6871 (tmm) cc_final: 0.6475 (tmm) REVERT: E 461 SER cc_start: 0.8513 (t) cc_final: 0.8164 (t) REVERT: F 166 ARG cc_start: 0.8325 (mtt90) cc_final: 0.8088 (mmt90) REVERT: F 194 TYR cc_start: 0.7556 (m-80) cc_final: 0.7241 (m-80) REVERT: F 234 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8211 (mt-10) REVERT: F 247 PHE cc_start: 0.8670 (m-80) cc_final: 0.8376 (m-10) REVERT: F 372 PRO cc_start: 0.9186 (Cg_endo) cc_final: 0.8918 (Cg_exo) REVERT: F 392 PHE cc_start: 0.8784 (t80) cc_final: 0.8575 (t80) REVERT: F 457 LYS cc_start: 0.8968 (pttp) cc_final: 0.8647 (pttp) REVERT: F 458 MET cc_start: 0.7172 (tmm) cc_final: 0.6649 (tmm) outliers start: 80 outliers final: 68 residues processed: 629 average time/residue: 0.1497 time to fit residues: 149.4931 Evaluate side-chains 623 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 552 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 228 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN B 429 HIS ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 429 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** 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 = 0.3730 r_free = 0.3730 target = 0.150913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120313 restraints weight = 38382.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.124141 restraints weight = 21509.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126719 restraints weight = 14569.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128479 restraints weight = 11213.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129488 restraints weight = 9363.415| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23454 Z= 0.149 Angle : 0.632 9.373 31680 Z= 0.318 Chirality : 0.045 0.163 3534 Planarity : 0.004 0.043 4062 Dihedral : 10.055 114.489 3456 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.09 % Allowed : 20.82 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.16), residues: 2880 helix: 1.21 (0.16), residues: 1050 sheet: -0.28 (0.20), residues: 720 loop : -0.15 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 385 TYR 0.033 0.002 TYR F 402 PHE 0.036 0.002 PHE C 392 TRP 0.011 0.001 TRP A 92 HIS 0.018 0.002 HIS E 429 Details of bonding type rmsd covalent geometry : bond 0.00338 (23448) covalent geometry : angle 0.63184 (31680) hydrogen bonds : bond 0.03072 ( 1134) hydrogen bonds : angle 4.62146 ( 3060) Misc. bond : bond 0.00029 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 585 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8751 (mmt180) cc_final: 0.8469 (mmt90) REVERT: A 235 TYR cc_start: 0.8723 (m-80) cc_final: 0.8229 (m-80) REVERT: A 420 MET cc_start: 0.6078 (OUTLIER) cc_final: 0.5531 (tpp) REVERT: A 457 LYS cc_start: 0.8717 (pttp) cc_final: 0.8512 (pttp) REVERT: B 166 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7605 (ptp-170) REVERT: B 170 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7677 (mtm180) REVERT: B 187 GLU cc_start: 0.6815 (mp0) cc_final: 0.6577 (mp0) REVERT: B 216 ARG cc_start: 0.8845 (mmt180) cc_final: 0.8513 (mmt90) REVERT: B 234 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 394 GLN cc_start: 0.8386 (mt0) cc_final: 0.7812 (mp10) REVERT: B 402 TYR cc_start: 0.8835 (t80) cc_final: 0.8557 (t80) REVERT: C 161 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8156 (tpp80) REVERT: C 185 ILE cc_start: 0.9168 (mt) cc_final: 0.8903 (mm) REVERT: C 187 GLU cc_start: 0.6935 (mp0) cc_final: 0.6573 (mp0) REVERT: C 194 TYR cc_start: 0.7538 (m-80) cc_final: 0.7225 (m-80) REVERT: C 221 GLU cc_start: 0.7361 (tt0) cc_final: 0.6993 (tt0) REVERT: C 234 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8240 (mt-10) REVERT: C 247 PHE cc_start: 0.8627 (m-80) cc_final: 0.8306 (m-10) REVERT: C 372 PRO cc_start: 0.9191 (Cg_endo) cc_final: 0.8900 (Cg_exo) REVERT: D 162 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7888 (tpt90) REVERT: D 166 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7352 (mtt180) REVERT: D 194 TYR cc_start: 0.7588 (m-80) cc_final: 0.7304 (m-80) REVERT: D 235 TYR cc_start: 0.8774 (m-80) cc_final: 0.8398 (m-80) REVERT: D 457 LYS cc_start: 0.9111 (ptmm) cc_final: 0.8691 (pttp) REVERT: E 170 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7711 (mtm180) REVERT: E 187 GLU cc_start: 0.6824 (mp0) cc_final: 0.6458 (mp0) REVERT: E 188 TYR cc_start: 0.8524 (m-80) cc_final: 0.8297 (m-10) REVERT: E 216 ARG cc_start: 0.8903 (mmt180) cc_final: 0.8568 (mmt90) REVERT: E 234 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7943 (mt-10) REVERT: E 304 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8731 (t0) REVERT: E 394 GLN cc_start: 0.8450 (mt0) cc_final: 0.7914 (mp10) REVERT: E 420 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5374 (ttp) REVERT: E 458 MET cc_start: 0.6611 (tmm) cc_final: 0.6160 (tmm) REVERT: E 461 SER cc_start: 0.8329 (t) cc_final: 0.7999 (t) REVERT: F 166 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7994 (mmt90) REVERT: F 187 GLU cc_start: 0.7005 (mp0) cc_final: 0.6685 (mp0) REVERT: F 194 TYR cc_start: 0.7514 (m-80) cc_final: 0.7235 (m-80) REVERT: F 234 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8206 (mt-10) REVERT: F 372 PRO cc_start: 0.9206 (Cg_endo) cc_final: 0.8931 (Cg_exo) REVERT: F 435 ASP cc_start: 0.7763 (t0) cc_final: 0.7493 (t0) REVERT: F 450 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7795 (p) REVERT: F 458 MET cc_start: 0.7118 (tmm) cc_final: 0.6781 (tmm) outliers start: 75 outliers final: 62 residues processed: 624 average time/residue: 0.1482 time to fit residues: 146.4642 Evaluate side-chains 626 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 559 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 164 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 308 ASN E 429 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** 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 = 0.3726 r_free = 0.3726 target = 0.150602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119850 restraints weight = 38856.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123672 restraints weight = 21771.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126239 restraints weight = 14817.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127988 restraints weight = 11405.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129113 restraints weight = 9534.115| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23454 Z= 0.166 Angle : 0.642 9.208 31680 Z= 0.323 Chirality : 0.046 0.173 3534 Planarity : 0.004 0.042 4062 Dihedral : 9.922 114.803 3456 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.00 % Allowed : 21.52 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2880 helix: 1.18 (0.16), residues: 1050 sheet: -0.30 (0.20), residues: 720 loop : -0.20 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 385 TYR 0.036 0.002 TYR C 402 PHE 0.022 0.002 PHE C 247 TRP 0.011 0.001 TRP C 92 HIS 0.016 0.002 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00387 (23448) covalent geometry : angle 0.64250 (31680) hydrogen bonds : bond 0.03065 ( 1134) hydrogen bonds : angle 4.65819 ( 3060) Misc. bond : bond 0.00024 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 564 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8754 (mmt180) cc_final: 0.8489 (mmt90) REVERT: A 235 TYR cc_start: 0.8716 (m-80) cc_final: 0.8215 (m-80) REVERT: B 166 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7744 (ptp-170) REVERT: B 170 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7648 (mtm180) REVERT: B 187 GLU cc_start: 0.6701 (mp0) cc_final: 0.6467 (mp0) REVERT: B 216 ARG cc_start: 0.8850 (mmt180) cc_final: 0.8515 (mmt90) REVERT: B 234 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 247 PHE cc_start: 0.8605 (m-80) cc_final: 0.8344 (m-10) REVERT: B 394 GLN cc_start: 0.8397 (mt0) cc_final: 0.7818 (mp10) REVERT: B 420 MET cc_start: 0.5787 (tpp) cc_final: 0.5514 (tpp) REVERT: C 185 ILE cc_start: 0.9170 (mt) cc_final: 0.8921 (mm) REVERT: C 187 GLU cc_start: 0.6882 (mp0) cc_final: 0.6574 (mp0) REVERT: C 194 TYR cc_start: 0.7532 (m-80) cc_final: 0.7246 (m-80) REVERT: C 221 GLU cc_start: 0.7370 (tt0) cc_final: 0.6980 (tt0) REVERT: C 234 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 372 PRO cc_start: 0.9178 (Cg_endo) cc_final: 0.8901 (Cg_exo) REVERT: C 420 MET cc_start: 0.5986 (tpp) cc_final: 0.5781 (tpp) REVERT: D 162 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7967 (tpt170) REVERT: D 235 TYR cc_start: 0.8766 (m-80) cc_final: 0.8377 (m-80) REVERT: D 319 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: D 457 LYS cc_start: 0.9068 (ptmm) cc_final: 0.8692 (pttp) REVERT: E 170 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7660 (mtm180) REVERT: E 187 GLU cc_start: 0.6756 (mp0) cc_final: 0.6400 (mp0) REVERT: E 188 TYR cc_start: 0.8549 (m-80) cc_final: 0.8319 (m-10) REVERT: E 216 ARG cc_start: 0.8941 (mmt180) cc_final: 0.8597 (mmt90) REVERT: E 234 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 345 LYS cc_start: 0.8578 (mtpp) cc_final: 0.7684 (ttpt) REVERT: E 394 GLN cc_start: 0.8471 (mt0) cc_final: 0.7954 (mp10) REVERT: E 420 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5339 (ttp) REVERT: E 458 MET cc_start: 0.6654 (tmm) cc_final: 0.6260 (tmm) REVERT: E 461 SER cc_start: 0.8356 (t) cc_final: 0.8035 (t) REVERT: F 166 ARG cc_start: 0.8264 (mtt90) cc_final: 0.7995 (mmt90) REVERT: F 187 GLU cc_start: 0.6888 (mp0) cc_final: 0.6626 (mp0) REVERT: F 194 TYR cc_start: 0.7477 (m-80) cc_final: 0.7220 (m-80) REVERT: F 234 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8194 (mt-10) REVERT: F 372 PRO cc_start: 0.9196 (Cg_endo) cc_final: 0.8939 (Cg_exo) REVERT: F 435 ASP cc_start: 0.7908 (t0) cc_final: 0.7640 (t0) REVERT: F 450 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.8052 (p) REVERT: F 458 MET cc_start: 0.7139 (tmm) cc_final: 0.6792 (tmm) outliers start: 73 outliers final: 65 residues processed: 600 average time/residue: 0.1488 time to fit residues: 142.4480 Evaluate side-chains 616 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 548 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 248 optimal weight: 0.0980 chunk 286 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 285 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 194 optimal weight: 0.0030 chunk 180 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120316 restraints weight = 38660.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124008 restraints weight = 21953.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126549 restraints weight = 15016.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128241 restraints weight = 11596.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129265 restraints weight = 9741.305| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23454 Z= 0.149 Angle : 0.634 9.063 31680 Z= 0.319 Chirality : 0.045 0.176 3534 Planarity : 0.004 0.042 4062 Dihedral : 9.788 115.493 3456 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.67 % Allowed : 22.47 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.16), residues: 2880 helix: 1.23 (0.16), residues: 1050 sheet: -0.42 (0.19), residues: 798 loop : -0.25 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.035 0.002 TYR F 402 PHE 0.019 0.002 PHE C 247 TRP 0.011 0.001 TRP C 92 HIS 0.016 0.002 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00344 (23448) covalent geometry : angle 0.63354 (31680) hydrogen bonds : bond 0.03005 ( 1134) hydrogen bonds : angle 4.60892 ( 3060) Misc. bond : bond 0.00024 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 565 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7766 (ptt) cc_final: 0.7530 (ptt) REVERT: A 216 ARG cc_start: 0.8755 (mmt180) cc_final: 0.8502 (mmt90) REVERT: A 235 TYR cc_start: 0.8701 (m-80) cc_final: 0.8187 (m-80) REVERT: A 450 SER cc_start: 0.8156 (t) cc_final: 0.7560 (p) REVERT: A 469 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 470 PHE cc_start: 0.7567 (p90) cc_final: 0.7270 (p90) REVERT: B 166 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7714 (ptp-170) REVERT: B 170 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7674 (mtm180) REVERT: B 187 GLU cc_start: 0.6705 (mp0) cc_final: 0.6488 (mp0) REVERT: B 216 ARG cc_start: 0.8835 (mmt180) cc_final: 0.8505 (mmt90) REVERT: B 234 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7848 (mt-10) REVERT: B 394 GLN cc_start: 0.8424 (mt0) cc_final: 0.7838 (mp10) REVERT: B 418 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7817 (mm-40) REVERT: C 161 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8157 (tpp80) REVERT: C 185 ILE cc_start: 0.9167 (mt) cc_final: 0.8913 (mm) REVERT: C 187 GLU cc_start: 0.6941 (mp0) cc_final: 0.6660 (mp0) REVERT: C 194 TYR cc_start: 0.7420 (m-80) cc_final: 0.7163 (m-80) REVERT: C 221 GLU cc_start: 0.7387 (tt0) cc_final: 0.6973 (tt0) REVERT: C 234 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8188 (mt-10) REVERT: C 372 PRO cc_start: 0.9179 (Cg_endo) cc_final: 0.8898 (Cg_exo) REVERT: C 457 LYS cc_start: 0.8915 (pttp) cc_final: 0.8694 (pttp) REVERT: D 162 ARG cc_start: 0.8273 (mmm160) cc_final: 0.7969 (tpt170) REVERT: D 181 THR cc_start: 0.9067 (m) cc_final: 0.8755 (m) REVERT: D 235 TYR cc_start: 0.8750 (m-80) cc_final: 0.8361 (m-80) REVERT: D 319 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: D 418 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7972 (mm110) REVERT: D 457 LYS cc_start: 0.9031 (ptmm) cc_final: 0.8677 (pttp) REVERT: E 170 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7661 (mtm180) REVERT: E 187 GLU cc_start: 0.6810 (mp0) cc_final: 0.6488 (mp0) REVERT: E 188 TYR cc_start: 0.8540 (m-80) cc_final: 0.8309 (m-10) REVERT: E 216 ARG cc_start: 0.8935 (mmt180) cc_final: 0.8603 (mmt90) REVERT: E 234 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7845 (mt-10) REVERT: E 345 LYS cc_start: 0.8624 (mtpp) cc_final: 0.7782 (ttpt) REVERT: E 394 GLN cc_start: 0.8480 (mt0) cc_final: 0.7901 (mp10) REVERT: E 458 MET cc_start: 0.6626 (tmm) cc_final: 0.6243 (tmm) REVERT: E 461 SER cc_start: 0.8359 (t) cc_final: 0.8032 (t) REVERT: F 166 ARG cc_start: 0.8294 (mtt90) cc_final: 0.7999 (mmt90) REVERT: F 187 GLU cc_start: 0.6915 (mp0) cc_final: 0.6627 (mp0) REVERT: F 194 TYR cc_start: 0.7481 (m-80) cc_final: 0.7226 (m-80) REVERT: F 234 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8180 (mt-10) REVERT: F 372 PRO cc_start: 0.9200 (Cg_endo) cc_final: 0.8939 (Cg_exo) REVERT: F 435 ASP cc_start: 0.7890 (t0) cc_final: 0.7647 (t0) REVERT: F 449 MET cc_start: 0.6027 (mmp) cc_final: 0.5791 (mmp) REVERT: F 450 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7979 (p) REVERT: F 458 MET cc_start: 0.7120 (tmm) cc_final: 0.6771 (tmm) outliers start: 65 outliers final: 59 residues processed: 598 average time/residue: 0.1514 time to fit residues: 144.3703 Evaluate side-chains 616 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 554 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 450 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 15 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 224 optimal weight: 0.3980 chunk 199 optimal weight: 0.0030 chunk 170 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121948 restraints weight = 38376.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125691 restraints weight = 21679.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128211 restraints weight = 14798.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129947 restraints weight = 11416.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131116 restraints weight = 9554.131| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23454 Z= 0.124 Angle : 0.618 9.236 31680 Z= 0.311 Chirality : 0.045 0.207 3534 Planarity : 0.004 0.046 4062 Dihedral : 9.532 116.769 3456 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.10 % Allowed : 23.50 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.16), residues: 2880 helix: 1.33 (0.16), residues: 1050 sheet: -0.20 (0.20), residues: 756 loop : -0.41 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 385 TYR 0.035 0.001 TYR F 402 PHE 0.028 0.002 PHE E 392 TRP 0.012 0.001 TRP C 92 HIS 0.016 0.002 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00277 (23448) covalent geometry : angle 0.61849 (31680) hydrogen bonds : bond 0.02840 ( 1134) hydrogen bonds : angle 4.47556 ( 3060) Misc. bond : bond 0.00019 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.54 seconds wall clock time: 72 minutes 5.63 seconds (4325.63 seconds total)