Starting phenix.real_space_refine on Sat Jul 4 19:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s67_24852/07_2026/7s67_24852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s67_24852/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s67_24852/07_2026/7s67_24852.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s67_24852/07_2026/7s67_24852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s67_24852/07_2026/7s67_24852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s67_24852/07_2026/7s67_24852.map" model { file = "/net/cci-nas-00/data/ceres_data/7s67_24852/07_2026/7s67_24852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s67_24852/07_2026/7s67_24852.cif" } 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-6108/lib/python3.11/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: 5.75, per 1000 atoms: 0.25 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: 2.01 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: 0.78 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: 5.14 Time building geometry restraints manager: 2.66 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: 13738 29.18 - 58.36: 224 58.36 - 87.54: 30 87.54 - 116.72: 6 116.72 - 145.90: 6 Dihedral angle restraints: 14004 sinusoidal: 5742 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 14001 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.300 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 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 : 11.904 145.899 8700 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/Z covalent geometry : bond 0.01306 / 0.71 (23448) covalent geometry : angle 1.39476 / 0.95 (31680) hydrogen bonds : bond 0.16785 / 11.02 ( 1134) hydrogen bonds : angle 7.08064 / 4.97 ( 3060) Misc. bond : bond 0.46646 / 24.80 ( 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 : 0.784 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: 0.1891 time to fit residues: 286.9131 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 : 0.790 ------------------------------------------------------------------------------- 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... 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 308 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.161614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131413 restraints weight = 37251.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135801 restraints weight = 20162.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138805 restraints weight = 13263.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140768 restraints weight = 9894.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.142090 restraints weight = 8082.724| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23454 Z= 0.182 Angle : 0.670 6.913 31680 Z= 0.356 Chirality : 0.047 0.170 3534 Planarity : 0.005 0.046 4062 Dihedral : 9.574 124.276 3270 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 2.22 % Allowed : 12.26 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 : 0.33 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 269 TYR 0.025 0.002 TYR C 442 PHE 0.023 0.002 PHE A 419 TRP 0.022 0.002 TRP F 331 HIS 0.019 0.003 HIS C 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (23448) covalent geometry : angle 0.67024 / 0.36 (31680) hydrogen bonds : bond 0.04395 / 2.90 ( 1134) hydrogen bonds : angle 5.06900 / 3.53 ( 3060) Misc. bond : bond 0.00114 / 0.06 ( 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 712 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 658 time to evaluate : 0.828 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 24 MET cc_start: 0.7426 (mmt) cc_final: 0.7195 (mmt) REVERT: A 234 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 235 TYR cc_start: 0.8833 (m-80) cc_final: 0.8452 (m-80) REVERT: A 269 ARG cc_start: 0.6530 (mtp85) cc_final: 0.5860 (ttm110) REVERT: A 393 ARG cc_start: 0.7924 (ptt-90) cc_final: 0.7625 (ptt-90) REVERT: A 459 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6824 (mtm-85) REVERT: B 132 TYR cc_start: 0.7159 (t80) cc_final: 0.6750 (t80) REVERT: B 234 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8143 (mt-10) REVERT: B 235 TYR cc_start: 0.8812 (m-80) cc_final: 0.8498 (m-80) REVERT: B 274 CYS cc_start: 0.8244 (m) cc_final: 0.8001 (t) REVERT: B 393 ARG cc_start: 0.7863 (ptt-90) cc_final: 0.7652 (ptt-90) REVERT: B 394 GLN cc_start: 0.8623 (mt0) cc_final: 0.7818 (mp10) REVERT: C 86 ASN cc_start: 0.8601 (m-40) cc_final: 0.8385 (m-40) REVERT: C 166 ARG cc_start: 0.8252 (mtt180) cc_final: 0.8032 (mtt180) REVERT: C 216 ARG cc_start: 0.8765 (mmt180) cc_final: 0.8424 (mmt90) REVERT: C 273 MET cc_start: 0.7597 (mtp) cc_final: 0.7310 (mtp) REVERT: C 304 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8002 (t0) REVERT: C 420 MET cc_start: 0.5814 (tpp) cc_final: 0.5446 (tpp) REVERT: D 234 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8224 (mt-10) REVERT: D 235 TYR cc_start: 0.8864 (m-80) cc_final: 0.8640 (m-80) REVERT: D 338 MET cc_start: 0.7942 (mmt) cc_final: 0.7416 (mmt) REVERT: D 393 ARG cc_start: 0.7959 (ptt-90) cc_final: 0.7713 (ptt-90) REVERT: D 420 MET cc_start: 0.5865 (tpp) cc_final: 0.5455 (tpp) REVERT: D 457 LYS cc_start: 0.9030 (ptmm) cc_final: 0.8730 (pttp) REVERT: D 459 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6975 (mtm-85) REVERT: D 469 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6935 (tm-30) REVERT: E 132 TYR cc_start: 0.7252 (t80) cc_final: 0.6916 (t80) REVERT: E 234 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 235 TYR cc_start: 0.8785 (m-80) cc_final: 0.8520 (m-80) REVERT: E 245 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8026 (m-40) REVERT: E 274 CYS cc_start: 0.8327 (m) cc_final: 0.8085 (t) REVERT: E 394 GLN cc_start: 0.8352 (mt0) cc_final: 0.7682 (mp10) REVERT: F 82 ASP cc_start: 0.8001 (m-30) cc_final: 0.7770 (m-30) REVERT: F 86 ASN cc_start: 0.8707 (m-40) cc_final: 0.8428 (m-40) REVERT: F 216 ARG cc_start: 0.8752 (mmt180) cc_final: 0.8402 (mmt90) REVERT: F 272 GLU cc_start: 0.8177 (pt0) cc_final: 0.7932 (mm-30) REVERT: F 273 MET cc_start: 0.7484 (mtp) cc_final: 0.7143 (mtp) REVERT: F 304 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8028 (t0) REVERT: F 442 TYR cc_start: 0.7632 (m-80) cc_final: 0.7272 (m-80) REVERT: F 454 ASN cc_start: 0.8042 (t0) cc_final: 0.7690 (t0) outliers start: 54 outliers final: 38 residues processed: 689 average time/residue: 0.1553 time to fit residues: 165.7791 Evaluate side-chains 595 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 554 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 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 304 ASN 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: 9.9990 chunk 194 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN B 429 HIS C 429 HIS C 463 HIS D 429 HIS D 463 HIS E 304 ASN E 429 HIS F 203 ASN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS F 463 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117663 restraints weight = 38762.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121495 restraints weight = 21569.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124081 restraints weight = 14539.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125848 restraints weight = 11093.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.126973 restraints weight = 9192.997| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 23454 Z= 0.329 Angle : 0.755 11.386 31680 Z= 0.389 Chirality : 0.050 0.164 3534 Planarity : 0.005 0.048 4062 Dihedral : 9.332 118.272 3270 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.79 % Allowed : 13.70 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.15), residues: 2880 helix: 0.59 (0.15), residues: 1050 sheet: -0.13 (0.19), residues: 786 loop : -0.09 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 162 TYR 0.026 0.003 TYR F 442 PHE 0.023 0.003 PHE E 59 TRP 0.032 0.003 TRP F 331 HIS 0.018 0.004 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.33 (23448) covalent geometry : angle 0.75455 / 0.39 (31680) hydrogen bonds : bond 0.04280 / 2.81 ( 1134) hydrogen bonds : angle 5.16425 / 3.59 ( 3060) Misc. bond : bond 0.00024 / 0.01 ( 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 663 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 571 time to evaluate : 0.808 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: 0.7477 (m-80) cc_final: 0.6958 (m-80) REVERT: A 203 ASN cc_start: 0.8779 (m-40) cc_final: 0.8321 (m110) REVERT: A 235 TYR cc_start: 0.8908 (m-80) cc_final: 0.8410 (m-80) REVERT: A 269 ARG cc_start: 0.6764 (mtp85) cc_final: 0.6185 (ttm110) REVERT: A 338 MET cc_start: 0.7995 (mmt) cc_final: 0.7489 (mmt) REVERT: A 469 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6767 (tm-30) REVERT: B 194 TYR cc_start: 0.7347 (m-80) cc_final: 0.6825 (m-80) REVERT: B 221 GLU cc_start: 0.7985 (tt0) cc_final: 0.7758 (tt0) REVERT: B 234 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 235 TYR cc_start: 0.8776 (m-80) cc_final: 0.8561 (m-80) REVERT: B 393 ARG cc_start: 0.7967 (ptt-90) cc_final: 0.7767 (ptt-90) REVERT: B 435 ASP cc_start: 0.7649 (t0) cc_final: 0.7293 (t0) REVERT: B 469 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7163 (tm-30) REVERT: C 191 ILE cc_start: 0.8284 (mp) cc_final: 0.7691 (mt) REVERT: C 194 TYR cc_start: 0.7648 (m-80) cc_final: 0.7021 (m-80) REVERT: C 203 ASN cc_start: 0.8730 (m-40) cc_final: 0.8131 (m-40) REVERT: C 216 ARG cc_start: 0.8784 (mmt180) cc_final: 0.8458 (mmt90) REVERT: C 420 MET cc_start: 0.6534 (tpp) cc_final: 0.6308 (tpp) REVERT: D 162 ARG cc_start: 0.8485 (mmm160) cc_final: 0.8228 (mmm160) REVERT: D 166 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7548 (mtt180) REVERT: D 194 TYR cc_start: 0.7463 (m-80) cc_final: 0.6972 (m-80) REVERT: D 234 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 235 TYR cc_start: 0.8949 (m-80) cc_final: 0.8624 (m-80) REVERT: D 274 CYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7874 (t) REVERT: D 338 MET cc_start: 0.7635 (mmt) cc_final: 0.7214 (mmt) REVERT: D 385 ARG cc_start: 0.8056 (ttm170) cc_final: 0.7820 (ttm170) REVERT: D 405 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 457 LYS cc_start: 0.9163 (ptmm) cc_final: 0.8874 (pttp) REVERT: E 194 TYR cc_start: 0.7386 (m-80) cc_final: 0.6905 (m-80) REVERT: E 203 ASN cc_start: 0.8927 (m-40) cc_final: 0.8607 (m-40) REVERT: E 221 GLU cc_start: 0.7954 (tt0) cc_final: 0.7740 (tt0) REVERT: E 234 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7949 (mt-10) REVERT: E 235 TYR cc_start: 0.8774 (m-80) cc_final: 0.8541 (m-80) REVERT: E 435 ASP cc_start: 0.7664 (t0) cc_final: 0.7423 (t0) REVERT: F 191 ILE cc_start: 0.8026 (mp) cc_final: 0.7579 (mt) REVERT: F 194 TYR cc_start: 0.7594 (m-80) cc_final: 0.7069 (m-80) REVERT: F 216 ARG cc_start: 0.8760 (mmt180) cc_final: 0.8413 (mmt90) REVERT: F 446 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.8171 (ptp90) REVERT: F 457 LYS cc_start: 0.8909 (pttp) cc_final: 0.8609 (pttp) outliers start: 92 outliers final: 77 residues processed: 616 average time/residue: 0.1494 time to fit residues: 143.3982 Evaluate side-chains 596 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 518 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 64 ILE 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 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 166 ARG 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 429 HIS 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 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 278 PHE 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 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 274 CYS 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 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 274 CYS Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 461 SER 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 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 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: 1.9990 chunk 10 optimal weight: 30.0000 chunk 200 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121024 restraints weight = 38313.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125070 restraints weight = 20948.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127778 restraints weight = 13902.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129578 restraints weight = 10470.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130653 restraints weight = 8630.362| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23454 Z= 0.136 Angle : 0.612 6.958 31680 Z= 0.314 Chirality : 0.046 0.151 3534 Planarity : 0.004 0.044 4062 Dihedral : 8.718 111.899 3270 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.92 % Allowed : 15.88 % 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: 0.34 (0.15), residues: 2880 helix: 0.89 (0.16), residues: 1050 sheet: -0.11 (0.19), residues: 786 loop : 0.02 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 162 TYR 0.032 0.002 TYR F 402 PHE 0.018 0.002 PHE D 59 TRP 0.018 0.002 TRP C 331 HIS 0.022 0.003 HIS E 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (23448) covalent geometry : angle 0.61214 / 0.31 (31680) hydrogen bonds : bond 0.03457 / 2.27 ( 1134) hydrogen bonds : angle 4.70864 / 3.28 ( 3060) Misc. bond : bond 0.00047 / 0.03 ( 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 679 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 608 time to evaluate : 0.836 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: 0.7545 (m-80) cc_final: 0.7061 (m-80) REVERT: A 235 TYR cc_start: 0.8746 (m-80) cc_final: 0.8264 (m-80) REVERT: A 269 ARG cc_start: 0.6789 (mtp85) cc_final: 0.6296 (ttm170) REVERT: A 385 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7619 (ttm170) REVERT: A 393 ARG cc_start: 0.7941 (ptt-90) cc_final: 0.7672 (ptt-90) REVERT: A 469 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6724 (tm-30) REVERT: B 194 TYR cc_start: 0.7440 (m-80) cc_final: 0.7004 (m-80) REVERT: B 203 ASN cc_start: 0.8771 (m-40) cc_final: 0.8352 (m110) REVERT: B 221 GLU cc_start: 0.7944 (tt0) cc_final: 0.7693 (tt0) REVERT: B 234 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 235 TYR cc_start: 0.8725 (m-80) cc_final: 0.8351 (m-80) REVERT: B 394 GLN cc_start: 0.8650 (mt0) cc_final: 0.7881 (mp10) REVERT: B 420 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5778 (tpp) REVERT: B 423 HIS cc_start: 0.5577 (t-90) cc_final: 0.5252 (t70) REVERT: B 435 ASP cc_start: 0.7678 (t0) cc_final: 0.7428 (t0) REVERT: C 194 TYR cc_start: 0.7524 (m-80) cc_final: 0.7096 (m-80) REVERT: C 234 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8246 (mt-10) REVERT: C 450 SER cc_start: 0.8108 (t) cc_final: 0.7821 (p) REVERT: C 457 LYS cc_start: 0.8774 (pttp) cc_final: 0.8532 (pttp) REVERT: D 162 ARG cc_start: 0.8401 (mmm160) cc_final: 0.7915 (tpt170) REVERT: D 166 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7359 (mtt180) REVERT: D 170 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7890 (ttt180) REVERT: D 194 TYR cc_start: 0.7474 (m-80) cc_final: 0.7123 (m-80) REVERT: D 234 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8221 (mt-10) REVERT: D 235 TYR cc_start: 0.8844 (m-80) cc_final: 0.8492 (m-80) REVERT: D 392 PHE cc_start: 0.8823 (t80) cc_final: 0.8598 (t80) REVERT: D 393 ARG cc_start: 0.8029 (ptt-90) cc_final: 0.7733 (ptt-90) REVERT: D 457 LYS cc_start: 0.8996 (ptmm) cc_final: 0.8743 (pttp) REVERT: E 194 TYR cc_start: 0.7342 (m-80) cc_final: 0.6897 (m-80) REVERT: E 203 ASN cc_start: 0.8874 (m-40) cc_final: 0.8326 (m110) REVERT: E 206 ILE cc_start: 0.9062 (mt) cc_final: 0.8861 (mt) REVERT: E 234 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8101 (mt-10) REVERT: E 235 TYR cc_start: 0.8732 (m-80) cc_final: 0.8407 (m-80) REVERT: E 304 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8420 (t0) REVERT: E 394 GLN cc_start: 0.8568 (mt0) cc_final: 0.7913 (mp10) REVERT: E 435 ASP cc_start: 0.7531 (t0) cc_final: 0.7280 (t0) REVERT: E 458 MET cc_start: 0.6796 (tmm) cc_final: 0.6592 (tmm) REVERT: F 181 THR cc_start: 0.9017 (m) cc_final: 0.8798 (m) REVERT: F 194 TYR cc_start: 0.7608 (m-80) cc_final: 0.7206 (m-80) REVERT: F 216 ARG cc_start: 0.8748 (mmt180) cc_final: 0.7952 (mmt90) REVERT: F 234 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8090 (mt-10) REVERT: F 315 PHE cc_start: 0.8929 (m-10) cc_final: 0.8716 (m-10) REVERT: F 372 PRO cc_start: 0.9201 (Cg_endo) cc_final: 0.8926 (Cg_exo) REVERT: F 457 LYS cc_start: 0.9063 (pttp) cc_final: 0.8776 (pttp) REVERT: F 458 MET cc_start: 0.7115 (tmm) cc_final: 0.6807 (tmm) outliers start: 71 outliers final: 58 residues processed: 645 average time/residue: 0.1449 time to fit residues: 147.3185 Evaluate side-chains 595 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 535 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 180 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 456 PHE 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 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 180 MET 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 290 THR 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 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 461 SER 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 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: 0.8980 chunk 99 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN ** 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 = 0.3736 r_free = 0.3736 target = 0.151353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121655 restraints weight = 38193.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125603 restraints weight = 20969.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128289 restraints weight = 13962.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130061 restraints weight = 10571.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131229 restraints weight = 8728.055| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23454 Z= 0.149 Angle : 0.609 8.728 31680 Z= 0.310 Chirality : 0.045 0.158 3534 Planarity : 0.004 0.044 4062 Dihedral : 8.456 113.393 3270 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.42 % Allowed : 17.86 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.46 (0.16), residues: 2880 helix: 1.08 (0.16), residues: 1050 sheet: -0.06 (0.20), residues: 708 loop : -0.02 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.031 0.002 TYR F 402 PHE 0.016 0.002 PHE A 59 TRP 0.029 0.002 TRP C 331 HIS 0.015 0.002 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (23448) covalent geometry : angle 0.60883 / 0.31 (31680) hydrogen bonds : bond 0.03260 / 2.14 ( 1134) hydrogen bonds : angle 4.65355 / 3.26 ( 3060) Misc. bond : bond 0.00038 / 0.02 ( 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 679 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 596 time to evaluate : 0.832 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: 0.7541 (m-80) cc_final: 0.7157 (m-80) REVERT: A 235 TYR cc_start: 0.8745 (m-80) cc_final: 0.8260 (m-80) REVERT: A 255 THR cc_start: 0.8233 (t) cc_final: 0.8012 (t) REVERT: A 269 ARG cc_start: 0.6921 (mtp85) cc_final: 0.6420 (ttm170) REVERT: A 385 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8016 (ttm170) REVERT: A 393 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7780 (ptt-90) REVERT: A 469 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6768 (tm-30) REVERT: B 203 ASN cc_start: 0.8788 (m-40) cc_final: 0.8278 (m110) REVERT: B 221 GLU cc_start: 0.7948 (tt0) cc_final: 0.7448 (tt0) REVERT: B 234 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7976 (mt-10) REVERT: B 235 TYR cc_start: 0.8741 (m-80) cc_final: 0.8404 (m-80) REVERT: B 394 GLN cc_start: 0.8536 (mt0) cc_final: 0.7893 (mp10) REVERT: B 420 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5809 (tpp) REVERT: B 435 ASP cc_start: 0.7661 (t0) cc_final: 0.7290 (t0) REVERT: C 185 ILE cc_start: 0.9148 (mt) cc_final: 0.8869 (mm) REVERT: C 194 TYR cc_start: 0.7595 (m-80) cc_final: 0.7194 (m-80) REVERT: C 234 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8232 (mt-10) REVERT: C 442 TYR cc_start: 0.7977 (m-80) cc_final: 0.7728 (m-80) REVERT: C 450 SER cc_start: 0.8106 (t) cc_final: 0.7893 (p) REVERT: C 457 LYS cc_start: 0.8762 (pttp) cc_final: 0.8519 (pttp) REVERT: C 458 MET cc_start: 0.7000 (tmm) cc_final: 0.6723 (tmm) REVERT: D 162 ARG cc_start: 0.8344 (mmm160) cc_final: 0.7891 (tpt90) REVERT: D 166 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7483 (mtt180) REVERT: D 194 TYR cc_start: 0.7476 (m-80) cc_final: 0.7186 (m-80) REVERT: D 235 TYR cc_start: 0.8857 (m-80) cc_final: 0.8475 (m-80) REVERT: D 247 PHE cc_start: 0.8689 (m-80) cc_final: 0.8408 (m-10) REVERT: D 361 GLN cc_start: 0.9009 (tp40) cc_final: 0.8786 (tp40) REVERT: D 385 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7656 (ttm170) REVERT: D 393 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7838 (ptt-90) REVERT: D 420 MET cc_start: 0.6713 (tpp) cc_final: 0.6452 (tpp) REVERT: D 469 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7180 (tm-30) REVERT: E 194 TYR cc_start: 0.7424 (m-80) cc_final: 0.6997 (m-80) REVERT: E 203 ASN cc_start: 0.8902 (m-40) cc_final: 0.8355 (m110) REVERT: E 234 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8056 (mt-10) REVERT: E 235 TYR cc_start: 0.8737 (m-80) cc_final: 0.8399 (m-80) REVERT: E 394 GLN cc_start: 0.8542 (mt0) cc_final: 0.7854 (mp10) REVERT: E 420 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5288 (ttp) REVERT: E 435 ASP cc_start: 0.7553 (t0) cc_final: 0.7279 (t0) REVERT: E 458 MET cc_start: 0.6882 (tmm) cc_final: 0.6519 (tmm) REVERT: F 194 TYR cc_start: 0.7540 (m-80) cc_final: 0.7181 (m-80) REVERT: F 234 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8077 (mt-10) REVERT: F 372 PRO cc_start: 0.9177 (Cg_endo) cc_final: 0.8871 (Cg_exo) REVERT: F 450 SER cc_start: 0.8300 (m) cc_final: 0.7944 (p) REVERT: F 457 LYS cc_start: 0.9005 (pttp) cc_final: 0.8752 (pttp) REVERT: F 458 MET cc_start: 0.7127 (tmm) cc_final: 0.6919 (tmm) outliers start: 83 outliers final: 64 residues processed: 641 average time/residue: 0.1378 time to fit residues: 140.3892 Evaluate side-chains 621 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 553 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 436 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 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 461 SER Chi-restraints excluded: chain C residue 47 THR 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 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 290 THR 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 420 MET Chi-restraints excluded: chain E residue 461 SER 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 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 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: 20.0000 chunk 216 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** 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 131 ASN C 304 ASN C 308 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS D 131 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 HIS D 463 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 304 ASN F 308 ASN ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.113376 restraints weight = 39630.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116976 restraints weight = 22594.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.119416 restraints weight = 15546.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121041 restraints weight = 12049.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122099 restraints weight = 10126.757| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 23454 Z= 0.391 Angle : 0.805 12.141 31680 Z= 0.414 Chirality : 0.051 0.217 3534 Planarity : 0.006 0.045 4062 Dihedral : 8.926 108.257 3270 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.40 % Allowed : 18.23 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 2880 helix: 0.64 (0.16), residues: 1050 sheet: -0.34 (0.18), residues: 762 loop : -0.69 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 170 TYR 0.036 0.003 TYR C 402 PHE 0.032 0.003 PHE B 392 TRP 0.022 0.002 TRP C 331 HIS 0.015 0.004 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00903 / 0.39 (23448) covalent geometry : angle 0.80511 / 0.41 (31680) hydrogen bonds : bond 0.04191 / 2.78 ( 1134) hydrogen bonds : angle 5.29341 / 3.70 ( 3060) Misc. bond : bond 0.00008 / 0.00 ( 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 657 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 550 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7751 (ttp80) REVERT: A 235 TYR cc_start: 0.8826 (m-80) cc_final: 0.8296 (m-80) REVERT: A 457 LYS cc_start: 0.8893 (pttp) cc_final: 0.8674 (pttp) REVERT: A 469 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6995 (tm-30) REVERT: B 166 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7591 (ptp-170) REVERT: B 170 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7586 (mtm180) REVERT: B 234 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7855 (mt-10) REVERT: B 235 TYR cc_start: 0.8741 (m-80) cc_final: 0.8348 (m-80) REVERT: B 435 ASP cc_start: 0.7817 (t0) cc_final: 0.7455 (t0) REVERT: B 442 TYR cc_start: 0.8202 (m-80) cc_final: 0.7860 (m-10) REVERT: C 170 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7894 (mtm180) REVERT: C 194 TYR cc_start: 0.7668 (m-80) cc_final: 0.7294 (m-80) REVERT: C 217 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.8130 (ttt-90) REVERT: C 234 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 457 LYS cc_start: 0.9054 (pttp) cc_final: 0.8757 (pttp) REVERT: C 458 MET cc_start: 0.7368 (tmm) cc_final: 0.7080 (tmm) REVERT: D 86 ASN cc_start: 0.8520 (m-40) cc_final: 0.8312 (m-40) REVERT: D 161 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8315 (tpp80) REVERT: D 162 ARG cc_start: 0.8478 (mmm160) cc_final: 0.8134 (tpt170) REVERT: D 166 ARG cc_start: 0.8178 (mtm180) cc_final: 0.7396 (mtt180) REVERT: D 235 TYR cc_start: 0.8853 (m-80) cc_final: 0.8492 (m-80) REVERT: D 361 GLN cc_start: 0.9175 (tp40) cc_final: 0.8749 (tp40) REVERT: D 393 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7800 (ptt-90) REVERT: D 457 LYS cc_start: 0.8878 (pttp) cc_final: 0.8657 (pttp) REVERT: E 170 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7591 (mtm180) REVERT: E 234 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7903 (mt-10) REVERT: E 235 TYR cc_start: 0.8722 (m-80) cc_final: 0.8335 (m-80) REVERT: E 345 LYS cc_start: 0.8721 (mtpp) cc_final: 0.7824 (ttpt) REVERT: E 348 CYS cc_start: 0.8829 (m) cc_final: 0.8446 (m) REVERT: E 435 ASP cc_start: 0.7747 (t0) cc_final: 0.7281 (t0) REVERT: E 456 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8254 (t80) REVERT: E 458 MET cc_start: 0.7167 (tmm) cc_final: 0.6654 (tmm) REVERT: F 166 ARG cc_start: 0.8299 (mtt90) cc_final: 0.8045 (mmt90) REVERT: F 194 TYR cc_start: 0.7727 (m-80) cc_final: 0.7316 (m-80) REVERT: F 234 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8089 (mt-10) REVERT: F 372 PRO cc_start: 0.9265 (Cg_endo) cc_final: 0.9003 (Cg_exo) REVERT: F 458 MET cc_start: 0.7460 (tmm) cc_final: 0.7095 (tmm) outliers start: 107 outliers final: 86 residues processed: 605 average time/residue: 0.1423 time to fit residues: 135.7562 Evaluate side-chains 612 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 522 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 161 ARG 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 324 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 443 VAL 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 154 TYR 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 461 SER Chi-restraints excluded: chain C residue 47 THR 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 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 D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 147 VAL 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 161 ARG 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 429 HIS 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 365 SER Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 461 SER 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 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 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: 2.9990 chunk 235 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 263 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 245 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119207 restraints weight = 38453.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123009 restraints weight = 21412.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125583 restraints weight = 14512.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127346 restraints weight = 11133.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128335 restraints weight = 9261.681| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23454 Z= 0.143 Angle : 0.641 11.147 31680 Z= 0.326 Chirality : 0.045 0.187 3534 Planarity : 0.004 0.043 4062 Dihedral : 8.414 112.991 3270 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.09 % Allowed : 20.21 % Favored : 76.71 % 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: 0.22 (0.16), residues: 2880 helix: 1.05 (0.16), residues: 1050 sheet: -0.35 (0.19), residues: 720 loop : -0.23 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 216 TYR 0.039 0.002 TYR A 402 PHE 0.034 0.002 PHE F 392 TRP 0.013 0.002 TRP A 92 HIS 0.025 0.003 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (23448) covalent geometry : angle 0.64107 / 0.33 (31680) hydrogen bonds : bond 0.03259 / 2.15 ( 1134) hydrogen bonds : angle 4.73237 / 3.32 ( 3060) Misc. bond : bond 0.00050 / 0.03 ( 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 680 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 605 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7414 (ttp80) REVERT: A 235 TYR cc_start: 0.8668 (m-80) cc_final: 0.8128 (m-80) REVERT: A 457 LYS cc_start: 0.8684 (pttp) cc_final: 0.8481 (pttp) REVERT: A 469 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6935 (tm-30) REVERT: B 166 ARG cc_start: 0.7970 (ptp-170) cc_final: 0.7733 (ptp-170) REVERT: B 216 ARG cc_start: 0.8876 (mmt180) cc_final: 0.8520 (mmt90) REVERT: B 234 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 235 TYR cc_start: 0.8743 (m-80) cc_final: 0.8276 (m-80) REVERT: B 394 GLN cc_start: 0.8364 (mt0) cc_final: 0.7835 (mp10) REVERT: B 435 ASP cc_start: 0.7873 (t0) cc_final: 0.7599 (t0) REVERT: C 194 TYR cc_start: 0.7568 (m-80) cc_final: 0.7270 (m-80) REVERT: C 234 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8152 (mt-10) REVERT: C 372 PRO cc_start: 0.9189 (Cg_endo) cc_final: 0.8912 (Cg_exo) REVERT: C 457 LYS cc_start: 0.9029 (pttp) cc_final: 0.8751 (pttp) REVERT: D 86 ASN cc_start: 0.8527 (m-40) cc_final: 0.8300 (m-40) REVERT: D 162 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7886 (tpt90) REVERT: D 166 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7354 (mtt180) REVERT: D 194 TYR cc_start: 0.7615 (m-80) cc_final: 0.7281 (m-80) REVERT: D 235 TYR cc_start: 0.8797 (m-80) cc_final: 0.8313 (m-80) REVERT: D 247 PHE cc_start: 0.8834 (m-80) cc_final: 0.8403 (m-10) REVERT: D 361 GLN cc_start: 0.9094 (tp40) cc_final: 0.8790 (tp40) REVERT: D 393 ARG cc_start: 0.7994 (ptt-90) cc_final: 0.7776 (ptt-90) REVERT: D 457 LYS cc_start: 0.8745 (pttp) cc_final: 0.8524 (pttp) REVERT: D 469 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7488 (tm-30) REVERT: E 170 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7661 (mtm180) REVERT: E 234 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7848 (mt-10) REVERT: E 235 TYR cc_start: 0.8738 (m-80) cc_final: 0.8249 (m-80) REVERT: E 304 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8519 (t0) REVERT: E 345 LYS cc_start: 0.8659 (mtpp) cc_final: 0.7787 (ttpt) REVERT: E 435 ASP cc_start: 0.7779 (t0) cc_final: 0.7451 (t0) REVERT: E 442 TYR cc_start: 0.7921 (m-10) cc_final: 0.7675 (m-10) REVERT: E 458 MET cc_start: 0.6872 (tmm) cc_final: 0.6456 (tmm) REVERT: F 166 ARG cc_start: 0.8229 (mtt90) cc_final: 0.7942 (mmt90) REVERT: F 194 TYR cc_start: 0.7583 (m-80) cc_final: 0.7240 (m-80) REVERT: F 234 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8199 (mt-10) REVERT: F 372 PRO cc_start: 0.9183 (Cg_endo) cc_final: 0.8895 (Cg_exo) REVERT: F 457 LYS cc_start: 0.9029 (pttp) cc_final: 0.8732 (pttp) REVERT: F 458 MET cc_start: 0.7252 (tmm) cc_final: 0.6754 (tmm) outliers start: 75 outliers final: 58 residues processed: 646 average time/residue: 0.1396 time to fit residues: 143.3372 Evaluate side-chains 618 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 558 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 161 ARG Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 443 VAL 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 185 ILE 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 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 274 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU 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 365 SER Chi-restraints excluded: chain D residue 429 HIS 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 290 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 461 SER 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 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU 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 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: 9.9990 chunk 255 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 231 optimal weight: 0.4980 chunk 234 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.147829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117697 restraints weight = 38607.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121446 restraints weight = 21734.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123973 restraints weight = 14789.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125690 restraints weight = 11369.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126657 restraints weight = 9505.788| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23454 Z= 0.182 Angle : 0.654 9.387 31680 Z= 0.331 Chirality : 0.046 0.184 3534 Planarity : 0.004 0.042 4062 Dihedral : 8.363 114.284 3270 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.92 % Allowed : 21.23 % Favored : 75.84 % 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: 0.18 (0.16), residues: 2880 helix: 1.10 (0.16), residues: 1050 sheet: -0.39 (0.20), residues: 720 loop : -0.32 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 170 TYR 0.041 0.002 TYR A 402 PHE 0.032 0.002 PHE C 247 TRP 0.012 0.001 TRP C 331 HIS 0.016 0.003 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (23448) covalent geometry : angle 0.65372 / 0.33 (31680) hydrogen bonds : bond 0.03283 / 2.17 ( 1134) hydrogen bonds : angle 4.74143 / 3.31 ( 3060) Misc. bond : bond 0.00026 / 0.01 ( 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 646 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 575 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8699 (m-80) cc_final: 0.8215 (m-80) REVERT: A 352 GLU cc_start: 0.8684 (mp0) cc_final: 0.8452 (mp0) REVERT: A 385 ARG cc_start: 0.8281 (ttm170) cc_final: 0.8019 (ttm170) REVERT: A 457 LYS cc_start: 0.8684 (pttp) cc_final: 0.8476 (pttp) REVERT: A 469 GLU cc_start: 0.7393 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 166 ARG cc_start: 0.7938 (ptp-170) cc_final: 0.7693 (ptp-170) REVERT: B 170 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7683 (mtm180) REVERT: B 187 GLU cc_start: 0.6830 (mp0) cc_final: 0.6600 (mp0) REVERT: B 216 ARG cc_start: 0.8856 (mmt180) cc_final: 0.8529 (mmt90) REVERT: B 234 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 235 TYR cc_start: 0.8809 (m-80) cc_final: 0.8297 (m-80) REVERT: B 394 GLN cc_start: 0.8398 (mt0) cc_final: 0.7862 (mp10) REVERT: B 418 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7935 (mm-40) REVERT: B 435 ASP cc_start: 0.7872 (t0) cc_final: 0.7551 (t0) REVERT: C 185 ILE cc_start: 0.9192 (mt) cc_final: 0.8915 (mm) REVERT: C 187 GLU cc_start: 0.6866 (mp0) cc_final: 0.6511 (mp0) REVERT: C 194 TYR cc_start: 0.7507 (m-80) cc_final: 0.7198 (m-80) REVERT: C 221 GLU cc_start: 0.7320 (tt0) cc_final: 0.6955 (tt0) REVERT: C 234 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8222 (mt-10) REVERT: C 372 PRO cc_start: 0.9195 (Cg_endo) cc_final: 0.8922 (Cg_exo) REVERT: C 457 LYS cc_start: 0.9052 (pttp) cc_final: 0.8762 (pttp) REVERT: D 162 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7970 (tpt170) REVERT: D 166 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7231 (mtt180) REVERT: D 194 TYR cc_start: 0.7614 (m-80) cc_final: 0.7318 (m-80) REVERT: D 235 TYR cc_start: 0.8762 (m-80) cc_final: 0.8352 (m-80) REVERT: D 247 PHE cc_start: 0.8856 (m-80) cc_final: 0.8275 (m-10) REVERT: D 361 GLN cc_start: 0.9147 (tp40) cc_final: 0.8738 (tp40) REVERT: D 393 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7817 (ptt-90) REVERT: D 469 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7364 (tm-30) REVERT: E 170 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7683 (mtm180) REVERT: E 187 GLU cc_start: 0.6825 (mp0) cc_final: 0.6569 (mp0) REVERT: E 234 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7894 (mt-10) REVERT: E 235 TYR cc_start: 0.8813 (m-80) cc_final: 0.8293 (m-80) REVERT: E 435 ASP cc_start: 0.7822 (t0) cc_final: 0.7495 (t0) REVERT: E 449 MET cc_start: 0.7039 (mmt) cc_final: 0.6667 (mmp) REVERT: E 450 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7912 (p) REVERT: E 458 MET cc_start: 0.6952 (tmm) cc_final: 0.6478 (tmm) REVERT: F 166 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7924 (mmt90) REVERT: F 194 TYR cc_start: 0.7490 (m-80) cc_final: 0.7173 (m-80) REVERT: F 234 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8179 (mt-10) REVERT: F 247 PHE cc_start: 0.8508 (m-80) cc_final: 0.8251 (m-80) REVERT: F 372 PRO cc_start: 0.9195 (Cg_endo) cc_final: 0.8908 (Cg_exo) REVERT: F 450 SER cc_start: 0.8393 (m) cc_final: 0.8084 (p) REVERT: F 458 MET cc_start: 0.7207 (tmm) cc_final: 0.6795 (tmm) outliers start: 71 outliers final: 59 residues processed: 618 average time/residue: 0.1361 time to fit residues: 133.5130 Evaluate side-chains 608 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 547 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 365 SER 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 185 ILE 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 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 274 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU 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 365 SER Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 423 HIS 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 221 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 450 SER Chi-restraints excluded: chain E residue 461 SER 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 436 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 164 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 41 optimal weight: 0.0270 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 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** ** F 454 ASN ** 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 = 0.3707 r_free = 0.3707 target = 0.148059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117580 restraints weight = 39023.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121336 restraints weight = 21773.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123855 restraints weight = 14771.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125582 restraints weight = 11376.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.126562 restraints weight = 9554.035| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23454 Z= 0.183 Angle : 0.658 9.044 31680 Z= 0.332 Chirality : 0.046 0.212 3534 Planarity : 0.004 0.047 4062 Dihedral : 8.307 115.197 3270 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.88 % Allowed : 21.77 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2880 helix: 1.12 (0.16), residues: 1050 sheet: -0.32 (0.20), residues: 702 loop : -0.38 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 385 TYR 0.046 0.002 TYR A 402 PHE 0.039 0.002 PHE C 392 TRP 0.012 0.001 TRP C 331 HIS 0.017 0.003 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (23448) covalent geometry : angle 0.65805 / 0.33 (31680) hydrogen bonds : bond 0.03213 / 2.11 ( 1134) hydrogen bonds : angle 4.76947 / 3.33 ( 3060) Misc. bond : bond 0.00024 / 0.01 ( 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 635 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 565 time to evaluate : 0.853 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 21 MET cc_start: 0.8056 (ptt) cc_final: 0.7848 (ptt) REVERT: A 235 TYR cc_start: 0.8694 (m-80) cc_final: 0.8204 (m-80) REVERT: A 457 LYS cc_start: 0.8691 (pttp) cc_final: 0.8488 (pttp) REVERT: A 469 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6964 (tm-30) REVERT: B 166 ARG cc_start: 0.7931 (ptp-170) cc_final: 0.7674 (ptp-170) REVERT: B 170 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7691 (mtm180) REVERT: B 187 GLU cc_start: 0.6803 (mp0) cc_final: 0.6583 (mp0) REVERT: B 216 ARG cc_start: 0.8821 (mmt180) cc_final: 0.8497 (mmt90) REVERT: B 234 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 235 TYR cc_start: 0.8782 (m-80) cc_final: 0.8273 (m-80) REVERT: B 394 GLN cc_start: 0.8373 (mt0) cc_final: 0.7856 (mp10) REVERT: B 435 ASP cc_start: 0.7970 (t0) cc_final: 0.7681 (t0) REVERT: B 450 SER cc_start: 0.8041 (m) cc_final: 0.7761 (p) REVERT: B 461 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8384 (t) REVERT: C 166 ARG cc_start: 0.8253 (mmt90) cc_final: 0.7233 (mmt90) REVERT: C 185 ILE cc_start: 0.9205 (mt) cc_final: 0.8937 (mm) REVERT: C 187 GLU cc_start: 0.6915 (mp0) cc_final: 0.6538 (mp0) REVERT: C 194 TYR cc_start: 0.7465 (m-80) cc_final: 0.7156 (m-80) REVERT: C 221 GLU cc_start: 0.7354 (tt0) cc_final: 0.6959 (tt0) REVERT: C 234 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 372 PRO cc_start: 0.9177 (Cg_endo) cc_final: 0.8899 (Cg_exo) REVERT: D 162 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7995 (tpt170) REVERT: D 247 PHE cc_start: 0.8873 (m-80) cc_final: 0.8311 (m-10) REVERT: D 361 GLN cc_start: 0.9090 (tp40) cc_final: 0.8650 (tp40) REVERT: D 393 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7866 (ptt-90) REVERT: D 457 LYS cc_start: 0.8783 (pttp) cc_final: 0.8551 (pttp) REVERT: D 469 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7394 (tm-30) REVERT: E 170 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7662 (mtm180) REVERT: E 187 GLU cc_start: 0.6764 (mp0) cc_final: 0.6404 (mp0) REVERT: E 188 TYR cc_start: 0.8560 (m-80) cc_final: 0.8330 (m-10) REVERT: E 234 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7806 (mt-10) REVERT: E 235 TYR cc_start: 0.8807 (m-80) cc_final: 0.8268 (m-80) REVERT: E 304 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8354 (t0) REVERT: E 394 GLN cc_start: 0.8344 (mt0) cc_final: 0.7918 (mp10) REVERT: E 402 TYR cc_start: 0.8741 (t80) cc_final: 0.8323 (t80) REVERT: E 435 ASP cc_start: 0.7786 (t0) cc_final: 0.7470 (t0) REVERT: E 450 SER cc_start: 0.8267 (OUTLIER) cc_final: 0.7917 (p) REVERT: E 458 MET cc_start: 0.6928 (tmm) cc_final: 0.6430 (tmm) REVERT: F 166 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7835 (mmt90) REVERT: F 187 GLU cc_start: 0.6875 (mp0) cc_final: 0.6572 (mp0) REVERT: F 194 TYR cc_start: 0.7595 (m-80) cc_final: 0.7292 (m-80) REVERT: F 234 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8153 (mt-10) REVERT: F 372 PRO cc_start: 0.9200 (Cg_endo) cc_final: 0.8921 (Cg_exo) REVERT: F 385 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7966 (ttm170) REVERT: F 442 TYR cc_start: 0.7786 (m-10) cc_final: 0.7519 (m-10) REVERT: F 457 LYS cc_start: 0.9065 (pttp) cc_final: 0.8790 (pttp) REVERT: F 458 MET cc_start: 0.7198 (tmm) cc_final: 0.6723 (tmm) outliers start: 70 outliers final: 61 residues processed: 607 average time/residue: 0.1315 time to fit residues: 127.3762 Evaluate side-chains 613 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 548 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 274 CYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 443 VAL 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 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 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 274 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 443 VAL 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 180 MET Chi-restraints excluded: chain D residue 290 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 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 221 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 461 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 429 HIS ** 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 = 0.3703 r_free = 0.3703 target = 0.147619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117115 restraints weight = 38944.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120802 restraints weight = 22101.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123323 restraints weight = 15153.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124981 restraints weight = 11728.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126046 restraints weight = 9890.610| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23454 Z= 0.194 Angle : 0.667 8.727 31680 Z= 0.336 Chirality : 0.046 0.178 3534 Planarity : 0.004 0.045 4062 Dihedral : 8.298 115.619 3270 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.84 % Allowed : 22.26 % Favored : 74.90 % 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: 0.12 (0.16), residues: 2880 helix: 1.11 (0.16), residues: 1050 sheet: -0.41 (0.20), residues: 720 loop : -0.42 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 385 TYR 0.049 0.002 TYR A 402 PHE 0.019 0.002 PHE B 59 TRP 0.012 0.001 TRP C 331 HIS 0.018 0.003 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (23448) covalent geometry : angle 0.66686 / 0.34 (31680) hydrogen bonds : bond 0.03237 / 2.13 ( 1134) hydrogen bonds : angle 4.76115 / 3.32 ( 3060) Misc. bond : bond 0.00021 / 0.01 ( 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 628 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 559 time to evaluate : 0.797 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 235 TYR cc_start: 0.8698 (m-80) cc_final: 0.8209 (m-80) REVERT: A 352 GLU cc_start: 0.8702 (mp0) cc_final: 0.8280 (mp0) REVERT: A 385 ARG cc_start: 0.8201 (ttm170) cc_final: 0.7763 (ttm170) REVERT: B 166 ARG cc_start: 0.7948 (ptp-170) cc_final: 0.7636 (ptp-170) REVERT: B 170 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7658 (mtm180) REVERT: B 187 GLU cc_start: 0.6833 (mp0) cc_final: 0.6616 (mp0) REVERT: B 197 GLU cc_start: 0.8815 (mp0) cc_final: 0.8328 (mp0) REVERT: B 216 ARG cc_start: 0.8824 (mmt180) cc_final: 0.8492 (mmt90) REVERT: B 234 GLU cc_start: 0.8504 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 235 TYR cc_start: 0.8777 (m-80) cc_final: 0.8255 (m-80) REVERT: B 435 ASP cc_start: 0.7830 (t0) cc_final: 0.7520 (t0) REVERT: B 450 SER cc_start: 0.8233 (m) cc_final: 0.7936 (p) REVERT: B 456 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7970 (t80) REVERT: C 166 ARG cc_start: 0.8293 (mmt90) cc_final: 0.7365 (mmt90) REVERT: C 185 ILE cc_start: 0.9217 (mt) cc_final: 0.8943 (mm) REVERT: C 187 GLU cc_start: 0.6919 (mp0) cc_final: 0.6591 (mp0) REVERT: C 194 TYR cc_start: 0.7569 (m-80) cc_final: 0.7307 (m-80) REVERT: C 221 GLU cc_start: 0.7379 (tt0) cc_final: 0.6972 (tt0) REVERT: C 234 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 372 PRO cc_start: 0.9186 (Cg_endo) cc_final: 0.8920 (Cg_exo) REVERT: D 162 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7942 (tpt170) REVERT: D 247 PHE cc_start: 0.8896 (m-80) cc_final: 0.8331 (m-10) REVERT: D 361 GLN cc_start: 0.9132 (tp40) cc_final: 0.8695 (tp40) REVERT: D 393 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7767 (ptt-90) REVERT: D 457 LYS cc_start: 0.8777 (pttp) cc_final: 0.8544 (pttp) REVERT: D 469 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7357 (tm-30) REVERT: E 170 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7629 (mtm180) REVERT: E 187 GLU cc_start: 0.6801 (mp0) cc_final: 0.6448 (mp0) REVERT: E 188 TYR cc_start: 0.8590 (m-80) cc_final: 0.8355 (m-10) REVERT: E 234 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 235 TYR cc_start: 0.8799 (m-80) cc_final: 0.8256 (m-80) REVERT: E 394 GLN cc_start: 0.8509 (mt0) cc_final: 0.8042 (mp10) REVERT: E 402 TYR cc_start: 0.8778 (t80) cc_final: 0.8426 (t80) REVERT: E 435 ASP cc_start: 0.7721 (t0) cc_final: 0.7370 (t0) REVERT: E 450 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7776 (p) REVERT: E 458 MET cc_start: 0.6969 (tmm) cc_final: 0.6494 (tmm) REVERT: F 166 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7746 (mmt90) REVERT: F 187 GLU cc_start: 0.6877 (mp0) cc_final: 0.6601 (mp0) REVERT: F 194 TYR cc_start: 0.7580 (m-80) cc_final: 0.7278 (m-80) REVERT: F 234 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8159 (mt-10) REVERT: F 372 PRO cc_start: 0.9208 (Cg_endo) cc_final: 0.8930 (Cg_exo) REVERT: F 457 LYS cc_start: 0.9074 (pttp) cc_final: 0.8807 (pttp) REVERT: F 458 MET cc_start: 0.7158 (tmm) cc_final: 0.6829 (tmm) outliers start: 69 outliers final: 61 residues processed: 600 average time/residue: 0.1318 time to fit residues: 126.7861 Evaluate side-chains 613 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 549 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 274 CYS Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 443 VAL 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 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 456 PHE 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 274 CYS Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 147 VAL 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 290 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 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 221 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 461 SER 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 319 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 15 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 284 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 54 optimal weight: 0.0470 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 HIS ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 ASN ** D 429 HIS ** 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 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 = 0.3690 r_free = 0.3690 target = 0.146431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115962 restraints weight = 38938.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119623 restraints weight = 22174.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122064 restraints weight = 15221.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123669 restraints weight = 11829.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124770 restraints weight = 10005.688| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23454 Z= 0.227 Angle : 0.696 10.327 31680 Z= 0.352 Chirality : 0.047 0.176 3534 Planarity : 0.004 0.046 4062 Dihedral : 8.338 116.274 3270 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.05 % Allowed : 22.26 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.16), residues: 2880 helix: 1.12 (0.16), residues: 1050 sheet: -0.38 (0.20), residues: 702 loop : -0.56 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 385 TYR 0.047 0.002 TYR A 402 PHE 0.024 0.002 PHE D 392 TRP 0.013 0.002 TRP C 331 HIS 0.019 0.003 HIS B 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (23448) covalent geometry : angle 0.69615 / 0.35 (31680) hydrogen bonds : bond 0.03375 / 2.22 ( 1134) hydrogen bonds : angle 4.83220 / 3.37 ( 3060) Misc. bond : bond 0.00012 / 0.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.58 seconds wall clock time: 68 minutes 55.43 seconds (4135.43 seconds total)