Starting phenix.real_space_refine on Wed Nov 19 09:25:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s67_24852/11_2025/7s67_24852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s67_24852/11_2025/7s67_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s67_24852/11_2025/7s67_24852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s67_24852/11_2025/7s67_24852.map" model { file = "/net/cci-nas-00/data/ceres_data/7s67_24852/11_2025/7s67_24852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s67_24852/11_2025/7s67_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-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23058 Number of models: 1 Model: "" Number of chains: 8 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: "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} Restraints were copied for chains: B, C, D, E Time building chain proxies: 4.52, per 1000 atoms: 0.20 Number of scatterers: 23058 At special positions: 0 Unit cell: (118.45, 118.45, 109.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 30 15.00 Mg 12 11.99 O 4440 8.00 N 4056 7.00 C 14430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 274 " distance=0.00 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 306 " distance=0.00 Simple disulfide: pdb=" SG CYS B 348 " - pdb=" SG CYS B 348 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 981.9 milliseconds 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: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 371 Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.968A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.619A pdb=" N GLU A 432 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 156 through 175 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 293 through 308 Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 350 through 354 removed outlier: 3.638A pdb=" N ALA B 354 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 371 Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.968A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU B 432 " --> pdb=" O HIS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 156 through 175 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 293 through 308 Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA C 354 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 371 Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.969A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 406 Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU C 432 " --> pdb=" O HIS C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'D' and resid 27 through 32 Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 79 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 93 through 100 removed outlier: 3.607A pdb=" N LEU D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 Processing helix chain 'D' and resid 156 through 175 Processing helix chain 'D' and resid 196 through 201 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 267 through 274 Processing helix chain 'D' and resid 293 through 308 Processing helix chain 'D' and resid 320 through 330 Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA D 354 " --> pdb=" O PRO D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 371 Processing helix chain 'D' and resid 379 through 385 removed outlier: 3.969A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 406 Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU D 432 " --> pdb=" O HIS D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'E' and resid 27 through 32 Processing helix chain 'E' and resid 51 through 67 Processing helix chain 'E' and resid 79 through 88 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER E 124 " --> pdb=" O GLY E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 156 through 175 Processing helix chain 'E' and resid 196 through 201 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 267 through 274 Processing helix chain 'E' and resid 293 through 308 Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 334 through 341 Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.637A pdb=" N ALA E 354 " --> pdb=" O PRO E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 371 Processing helix chain 'E' and resid 379 through 385 removed outlier: 3.968A pdb=" N LEU E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 406 Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU E 432 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 79 through 88 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 93 through 100 removed outlier: 3.608A pdb=" N LEU F 97 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 137 removed outlier: 3.542A pdb=" N SER F 124 " --> pdb=" O GLY F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Processing helix chain 'F' and resid 156 through 175 Processing helix chain 'F' and resid 196 through 201 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 267 through 274 Processing helix chain 'F' and resid 293 through 308 Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 350 through 354 removed outlier: 3.638A pdb=" N ALA F 354 " --> pdb=" O PRO F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 371 Processing helix chain 'F' and resid 379 through 385 removed outlier: 3.969A pdb=" N LEU F 383 " --> pdb=" O SER F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.620A pdb=" N GLU F 432 " --> pdb=" O HIS F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN A 203 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG A 216 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ILE A 239 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG A 218 " --> pdb=" O PHE A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'A' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA A 312 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL A 347 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 314 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 413 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 284 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN A 414 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A 286 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER A 416 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY A 288 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 289 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR A 442 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET A 449 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE A 472 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU A 469 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 107 removed outlier: 4.077A pdb=" N ASN B 203 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 13.109A pdb=" N ARG B 216 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ILE B 239 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG B 218 " --> pdb=" O PHE B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA9, first strand: chain 'B' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA B 312 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 347 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 314 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 413 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE B 284 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN B 414 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 286 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER B 416 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY B 288 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 289 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 442 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET B 449 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE B 472 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU B 469 " --> pdb=" O LYS B 480 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN C 203 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG C 216 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ILE C 239 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG C 218 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AB5, first strand: chain 'C' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA C 312 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL C 347 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 314 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 413 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 284 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN C 414 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 286 " --> pdb=" O ASN C 414 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER C 416 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY C 288 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA C 289 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR C 442 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET C 449 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE C 472 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 469 " --> pdb=" O LYS C 480 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AB7, first strand: chain 'D' and resid 20 through 21 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN D 203 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG D 216 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N ILE D 239 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG D 218 " --> pdb=" O PHE D 237 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 262 through 263 Processing sheet with id=AC1, first strand: chain 'D' and resid 344 through 348 removed outlier: 6.931A pdb=" N ALA D 312 " --> pdb=" O LYS D 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL D 347 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU D 314 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR D 413 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE D 284 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN D 414 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA D 286 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER D 416 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY D 288 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA D 289 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR D 442 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N MET D 449 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N ILE D 472 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU D 469 " --> pdb=" O LYS D 480 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 486 through 487 Processing sheet with id=AC3, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'E' and resid 103 through 107 removed outlier: 4.076A pdb=" N ASN E 203 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 13.111A pdb=" N ARG E 216 " --> pdb=" O ILE E 239 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ILE E 239 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG E 218 " --> pdb=" O PHE E 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 262 through 263 Processing sheet with id=AC6, first strand: chain 'E' and resid 344 through 348 removed outlier: 6.931A pdb=" N ALA E 312 " --> pdb=" O LYS E 345 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL E 347 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU E 314 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 413 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE E 284 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN E 414 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 286 " --> pdb=" O ASN E 414 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER E 416 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY E 288 " --> pdb=" O SER E 416 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 289 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR E 442 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET E 449 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 9.731A pdb=" N ILE E 472 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N GLU E 469 " --> pdb=" O LYS E 480 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 486 through 487 Processing sheet with id=AC8, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC9, first strand: chain 'F' and resid 103 through 107 removed outlier: 4.077A pdb=" N ASN F 203 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 13.110A pdb=" N ARG F 216 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 9.701A pdb=" N ILE F 239 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG F 218 " --> pdb=" O PHE F 237 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 262 through 263 Processing sheet with id=AD2, first strand: chain 'F' and resid 344 through 348 removed outlier: 6.932A pdb=" N ALA F 312 " --> pdb=" O LYS F 345 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL F 347 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 314 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 413 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE F 284 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN F 414 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 286 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER F 416 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY F 288 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 289 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR F 442 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 13.471A pdb=" N MET F 449 " --> pdb=" O ILE F 472 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ILE F 472 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU F 469 " --> pdb=" O LYS F 480 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 486 through 487 1134 hydrogen bonds defined for protein. 3060 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.63 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: 13870 29.18 - 58.36: 272 58.36 - 87.54: 42 87.54 - 116.72: 6 116.72 - 145.90: 6 Dihedral angle restraints: 14196 sinusoidal: 5934 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 14193 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.720 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.516 23454 Z= 1.030 Angle : 1.395 21.283 31683 Z= 0.953 Chirality : 0.067 0.319 3534 Planarity : 0.011 0.072 4062 Dihedral : 12.758 145.899 8886 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 2880 helix: -0.43 (0.13), residues: 1038 sheet: 0.76 (0.21), residues: 696 loop : 0.65 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 451 TYR 0.109 0.015 TYR D 442 PHE 0.037 0.008 PHE E 237 TRP 0.066 0.018 TRP E 92 HIS 0.009 0.003 HIS F 423 Details of bonding type rmsd covalent geometry : bond 0.01306 (23448) covalent geometry : angle 1.39476 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.16785 ( 1134) hydrogen bonds : angle 7.08064 ( 3060) Misc. bond : bond 0.46646 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1032 time to evaluate : 0.898 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: 0.8123 (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: 0.7923 (mt-10) REVERT: F 247 PHE cc_start: 0.8586 (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: 0.2039 time to fit residues: 307.1750 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 : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 304 ASN A 327 ASN A 341 GLN A 368 ASN B 245 ASN B 260 ASN B 341 GLN B 342 ASN ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN C 341 GLN C 342 ASN C 368 ASN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS D 260 ASN D 304 ASN D 368 ASN D 463 HIS E 245 ASN E 260 ASN E 304 ASN E 341 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN F 341 GLN F 342 ASN F 368 ASN ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.161681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131562 restraints weight = 37196.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.135959 restraints weight = 20115.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.138964 restraints weight = 13209.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140940 restraints weight = 9837.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142315 restraints weight = 8009.404| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23454 Z= 0.173 Angle : 0.664 7.006 31683 Z= 0.351 Chirality : 0.047 0.174 3534 Planarity : 0.005 0.047 4062 Dihedral : 11.978 123.782 3456 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.30 % Allowed : 12.10 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.15), residues: 2880 helix: 0.59 (0.15), residues: 1050 sheet: 0.44 (0.20), residues: 714 loop : 0.34 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 161 TYR 0.022 0.002 TYR C 442 PHE 0.022 0.002 PHE A 419 TRP 0.018 0.002 TRP F 331 HIS 0.019 0.003 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00398 (23448) covalent geometry : angle 0.66435 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.04363 ( 1134) hydrogen bonds : angle 5.05744 ( 3060) Misc. bond : bond 0.00097 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 666 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7436 (mmt) cc_final: 0.7180 (mmt) REVERT: A 234 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8379 (mt-10) REVERT: A 235 TYR cc_start: 0.8835 (m-80) cc_final: 0.8455 (m-80) REVERT: A 269 ARG cc_start: 0.6531 (mtp85) cc_final: 0.5857 (ttm110) REVERT: A 393 ARG cc_start: 0.7905 (ptt-90) cc_final: 0.7626 (ptt-90) REVERT: A 420 MET cc_start: 0.5927 (tpp) cc_final: 0.5036 (tpp) REVERT: A 454 ASN cc_start: 0.8075 (t0) cc_final: 0.7710 (t0) REVERT: A 459 ARG cc_start: 0.7399 (mtt180) cc_final: 0.6828 (mtm-85) REVERT: B 132 TYR cc_start: 0.7172 (t80) cc_final: 0.6760 (t80) REVERT: B 234 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 235 TYR cc_start: 0.8812 (m-80) cc_final: 0.8498 (m-80) REVERT: B 393 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7652 (ptt-90) REVERT: B 394 GLN cc_start: 0.8639 (mt0) cc_final: 0.7855 (mp10) REVERT: C 86 ASN cc_start: 0.8605 (m-40) cc_final: 0.8405 (m-40) REVERT: C 166 ARG cc_start: 0.8251 (mtt180) cc_final: 0.8032 (mtt180) REVERT: C 216 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8426 (mmt90) REVERT: C 273 MET cc_start: 0.7603 (mtp) cc_final: 0.7315 (mtp) REVERT: C 304 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7977 (t0) REVERT: C 420 MET cc_start: 0.5753 (tpp) cc_final: 0.5050 (tpp) REVERT: D 162 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7844 (mmm160) REVERT: D 234 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8213 (mt-10) REVERT: D 235 TYR cc_start: 0.8866 (m-80) cc_final: 0.8512 (m-80) REVERT: D 338 MET cc_start: 0.7937 (mmt) cc_final: 0.7376 (mmt) REVERT: D 393 ARG cc_start: 0.7945 (ptt-90) cc_final: 0.7671 (ptt-90) REVERT: D 420 MET cc_start: 0.5881 (tpp) cc_final: 0.5465 (tpp) REVERT: D 457 LYS cc_start: 0.9029 (ptmm) cc_final: 0.8743 (pttp) REVERT: D 459 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6968 (mtm-85) REVERT: D 469 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6937 (tm-30) REVERT: E 132 TYR cc_start: 0.7257 (t80) cc_final: 0.6922 (t80) REVERT: E 166 ARG cc_start: 0.7624 (mtm180) cc_final: 0.7394 (mtm180) REVERT: E 234 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8105 (mt-10) REVERT: E 235 TYR cc_start: 0.8785 (m-80) cc_final: 0.8524 (m-80) REVERT: E 245 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: E 274 CYS cc_start: 0.8341 (m) cc_final: 0.8054 (t) REVERT: E 393 ARG cc_start: 0.7881 (ptt-90) cc_final: 0.7624 (ptt-90) REVERT: E 394 GLN cc_start: 0.8395 (mt0) cc_final: 0.7686 (mp10) REVERT: E 432 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8148 (mm-30) REVERT: E 461 SER cc_start: 0.8059 (t) cc_final: 0.7848 (t) REVERT: F 82 ASP cc_start: 0.7995 (m-30) cc_final: 0.7776 (m-30) REVERT: F 86 ASN cc_start: 0.8711 (m-40) cc_final: 0.8438 (m-40) REVERT: F 216 ARG cc_start: 0.8751 (mmt180) cc_final: 0.8402 (mmt90) REVERT: F 272 GLU cc_start: 0.8192 (pt0) cc_final: 0.7939 (mm-30) REVERT: F 273 MET cc_start: 0.7488 (mtp) cc_final: 0.7154 (mtp) REVERT: F 442 TYR cc_start: 0.7633 (m-80) cc_final: 0.7283 (m-80) REVERT: F 457 LYS cc_start: 0.8574 (pttp) cc_final: 0.8331 (pttp) outliers start: 56 outliers final: 40 residues processed: 699 average time/residue: 0.1675 time to fit residues: 180.0452 Evaluate side-chains 600 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 558 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 178 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 HIS ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 ASN 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 304 ASN F 308 ASN F 429 HIS F 463 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.147712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117730 restraints weight = 38691.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121616 restraints weight = 21414.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124238 restraints weight = 14339.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125989 restraints weight = 10931.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127033 restraints weight = 9062.587| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 23454 Z= 0.304 Angle : 0.740 11.626 31683 Z= 0.382 Chirality : 0.049 0.158 3534 Planarity : 0.005 0.046 4062 Dihedral : 12.100 115.342 3456 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.87 % Allowed : 13.70 % Favored : 82.43 % 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: 0.15 (0.15), residues: 2880 helix: 0.63 (0.15), residues: 1050 sheet: -0.16 (0.19), residues: 780 loop : 0.01 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 162 TYR 0.028 0.003 TYR A 402 PHE 0.023 0.003 PHE E 392 TRP 0.035 0.003 TRP C 331 HIS 0.018 0.004 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00698 (23448) covalent geometry : angle 0.73960 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.04130 ( 1134) hydrogen bonds : angle 5.13071 ( 3060) Misc. bond : bond 0.00029 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 578 time to evaluate : 0.766 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: 0.7548 (m-80) cc_final: 0.7075 (m-80) REVERT: A 235 TYR cc_start: 0.8901 (m-80) cc_final: 0.8391 (m-80) REVERT: A 269 ARG cc_start: 0.6747 (mtp85) cc_final: 0.6175 (ttm110) REVERT: A 274 CYS cc_start: 0.8321 (m) cc_final: 0.7865 (t) REVERT: A 338 MET cc_start: 0.7981 (mmt) cc_final: 0.7457 (mmt) REVERT: A 394 GLN cc_start: 0.8749 (mt0) cc_final: 0.8176 (mp10) REVERT: A 420 MET cc_start: 0.6325 (tpp) cc_final: 0.5447 (tpp) REVERT: A 469 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6784 (tm-30) REVERT: B 194 TYR cc_start: 0.7468 (m-80) cc_final: 0.6893 (m-80) REVERT: B 221 GLU cc_start: 0.7954 (tt0) cc_final: 0.7741 (tt0) REVERT: B 234 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7878 (mt-10) REVERT: B 235 TYR cc_start: 0.8756 (m-80) cc_final: 0.8540 (m-80) REVERT: B 469 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 191 ILE cc_start: 0.8222 (mp) cc_final: 0.7897 (mt) REVERT: C 194 TYR cc_start: 0.7676 (m-80) cc_final: 0.7060 (m-80) REVERT: C 216 ARG cc_start: 0.8770 (mmt180) cc_final: 0.8462 (mmt90) REVERT: C 385 ARG cc_start: 0.8188 (ttm170) cc_final: 0.7934 (ttm170) REVERT: C 392 PHE cc_start: 0.8802 (t80) cc_final: 0.8574 (t80) REVERT: C 393 ARG cc_start: 0.8035 (ptt-90) cc_final: 0.7825 (ptt-90) REVERT: D 194 TYR cc_start: 0.7435 (m-80) cc_final: 0.6965 (m-80) REVERT: D 235 TYR cc_start: 0.8889 (m-80) cc_final: 0.8544 (m-80) REVERT: D 274 CYS cc_start: 0.8414 (m) cc_final: 0.8200 (t) REVERT: D 457 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8861 (pttp) REVERT: E 194 TYR cc_start: 0.7395 (m-80) cc_final: 0.6877 (m-80) REVERT: E 203 ASN cc_start: 0.8919 (m-40) cc_final: 0.8600 (m-40) REVERT: E 221 GLU cc_start: 0.8031 (tt0) cc_final: 0.7773 (tt0) REVERT: E 234 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7958 (mt-10) REVERT: E 235 TYR cc_start: 0.8757 (m-80) cc_final: 0.8528 (m-80) REVERT: E 385 ARG cc_start: 0.8434 (ttm170) cc_final: 0.8226 (ttm170) REVERT: E 442 TYR cc_start: 0.7861 (m-80) cc_final: 0.7618 (m-80) REVERT: F 191 ILE cc_start: 0.8017 (mp) cc_final: 0.7569 (mt) REVERT: F 194 TYR cc_start: 0.7609 (m-80) cc_final: 0.7083 (m-80) REVERT: F 216 ARG cc_start: 0.8751 (mmt180) cc_final: 0.8405 (mmt90) REVERT: F 446 ARG cc_start: 0.8460 (ptp-110) cc_final: 0.8179 (ptp90) REVERT: F 457 LYS cc_start: 0.8988 (pttp) cc_final: 0.8680 (pttp) REVERT: F 469 GLU cc_start: 0.7489 (tt0) cc_final: 0.7140 (tm-30) outliers start: 94 outliers final: 78 residues processed: 625 average time/residue: 0.1682 time to fit residues: 162.8831 Evaluate side-chains 584 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 506 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 319 GLU Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 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 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 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 409 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 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 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: 6.9990 chunk 10 optimal weight: 30.0000 chunk 200 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN C 429 HIS D 463 HIS E 304 ASN ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN F 327 ASN F 429 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.148984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118905 restraints weight = 38548.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122837 restraints weight = 21199.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125524 restraints weight = 14181.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127288 restraints weight = 10751.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128385 restraints weight = 8902.913| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23454 Z= 0.198 Angle : 0.645 13.032 31683 Z= 0.331 Chirality : 0.047 0.171 3534 Planarity : 0.004 0.045 4062 Dihedral : 11.677 110.640 3456 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.54 % Allowed : 15.56 % Favored : 80.91 % 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: 0.16 (0.15), residues: 2880 helix: 0.81 (0.16), residues: 1050 sheet: -0.17 (0.19), residues: 786 loop : -0.19 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 40 TYR 0.036 0.002 TYR C 402 PHE 0.020 0.002 PHE D 59 TRP 0.018 0.002 TRP C 331 HIS 0.018 0.003 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00457 (23448) covalent geometry : angle 0.64521 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.03595 ( 1134) hydrogen bonds : angle 4.83583 ( 3060) Misc. bond : bond 0.00049 ( 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 666 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 580 time to evaluate : 1.068 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 162 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7831 (mmm160) REVERT: A 194 TYR cc_start: 0.7590 (m-80) cc_final: 0.7129 (m-80) REVERT: A 235 TYR cc_start: 0.8773 (m-80) cc_final: 0.8317 (m-80) REVERT: A 247 PHE cc_start: 0.8888 (m-80) cc_final: 0.8502 (m-10) REVERT: A 269 ARG cc_start: 0.6927 (mtp85) cc_final: 0.6439 (ttm170) REVERT: A 385 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7594 (ttm170) REVERT: A 393 ARG cc_start: 0.8022 (ptt-90) cc_final: 0.7702 (ptt-90) REVERT: A 469 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6887 (tm-30) REVERT: B 203 ASN cc_start: 0.8822 (m-40) cc_final: 0.8314 (m110) REVERT: B 221 GLU cc_start: 0.7924 (tt0) cc_final: 0.7687 (tt0) REVERT: B 234 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 235 TYR cc_start: 0.8761 (m-80) cc_final: 0.8368 (m-80) REVERT: B 394 GLN cc_start: 0.8627 (mt0) cc_final: 0.7971 (mp10) REVERT: B 420 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.5656 (tpp) REVERT: B 423 HIS cc_start: 0.5776 (t-90) cc_final: 0.5443 (t70) REVERT: B 435 ASP cc_start: 0.7621 (t0) cc_final: 0.7417 (t0) REVERT: C 170 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7938 (mtm180) REVERT: C 194 TYR cc_start: 0.7644 (m-80) cc_final: 0.7207 (m-80) REVERT: C 216 ARG cc_start: 0.8833 (mmt180) cc_final: 0.8599 (mmt90) REVERT: C 234 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 162 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8004 (tpt90) REVERT: D 166 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7401 (mtt180) REVERT: D 194 TYR cc_start: 0.7522 (m-80) cc_final: 0.7149 (m-80) REVERT: D 235 TYR cc_start: 0.8800 (m-80) cc_final: 0.8344 (m-80) REVERT: D 385 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7627 (ttm170) REVERT: D 393 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7784 (ptt-90) REVERT: E 203 ASN cc_start: 0.8934 (m-40) cc_final: 0.8395 (m110) REVERT: E 221 GLU cc_start: 0.7937 (tt0) cc_final: 0.7652 (tt0) REVERT: E 234 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7981 (mt-10) REVERT: E 235 TYR cc_start: 0.8749 (m-80) cc_final: 0.8298 (m-80) REVERT: E 304 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8490 (t0) REVERT: E 394 GLN cc_start: 0.8554 (mt0) cc_final: 0.7984 (mp10) REVERT: E 432 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8358 (mm-30) REVERT: F 191 ILE cc_start: 0.8173 (mp) cc_final: 0.7696 (mt) REVERT: F 194 TYR cc_start: 0.7708 (m-80) cc_final: 0.7272 (m-80) REVERT: F 216 ARG cc_start: 0.8791 (mmt180) cc_final: 0.8510 (mmt90) REVERT: F 234 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8037 (mt-10) REVERT: F 304 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8409 (t0) REVERT: F 315 PHE cc_start: 0.8924 (m-10) cc_final: 0.8697 (m-10) REVERT: F 372 PRO cc_start: 0.9205 (Cg_endo) cc_final: 0.8933 (Cg_exo) REVERT: F 457 LYS cc_start: 0.8931 (pttp) cc_final: 0.8686 (pttp) REVERT: F 458 MET cc_start: 0.7137 (tmm) cc_final: 0.6908 (tmm) outliers start: 86 outliers final: 68 residues processed: 626 average time/residue: 0.1660 time to fit residues: 162.1857 Evaluate side-chains 594 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 522 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 319 GLU 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 185 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 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 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 290 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 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 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 304 ASN Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 111 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 131 optimal weight: 0.0980 chunk 202 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** 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 ** 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 308 ASN ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.151588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121871 restraints weight = 38224.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125835 restraints weight = 20897.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128534 restraints weight = 13886.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130292 restraints weight = 10523.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131487 restraints weight = 8713.517| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23454 Z= 0.127 Angle : 0.603 8.929 31683 Z= 0.308 Chirality : 0.045 0.152 3534 Planarity : 0.004 0.043 4062 Dihedral : 10.968 112.833 3456 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.00 % Allowed : 17.41 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2880 helix: 1.11 (0.16), residues: 1050 sheet: -0.04 (0.20), residues: 708 loop : -0.05 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 138 TYR 0.036 0.002 TYR F 402 PHE 0.028 0.002 PHE C 392 TRP 0.011 0.001 TRP A 92 HIS 0.017 0.002 HIS E 429 Details of bonding type rmsd covalent geometry : bond 0.00284 (23448) covalent geometry : angle 0.60270 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.03233 ( 1134) hydrogen bonds : angle 4.60065 ( 3060) Misc. bond : bond 0.00041 ( 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 668 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 595 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7760 (mmm160) REVERT: A 194 TYR cc_start: 0.7596 (m-80) cc_final: 0.7199 (m-80) REVERT: A 216 ARG cc_start: 0.8853 (mmt180) cc_final: 0.8583 (mmt90) REVERT: A 235 TYR cc_start: 0.8715 (m-80) cc_final: 0.8210 (m-80) REVERT: A 269 ARG cc_start: 0.6937 (mtp85) cc_final: 0.6444 (ttm170) REVERT: A 392 PHE cc_start: 0.8792 (t80) cc_final: 0.8569 (t80) REVERT: A 393 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7668 (ptt-90) REVERT: A 420 MET cc_start: 0.6424 (tpp) cc_final: 0.5926 (tpp) REVERT: B 203 ASN cc_start: 0.8784 (m-40) cc_final: 0.8297 (m110) REVERT: B 221 GLU cc_start: 0.7941 (tt0) cc_final: 0.7338 (tt0) REVERT: B 234 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 235 TYR cc_start: 0.8709 (m-80) cc_final: 0.8316 (m-80) REVERT: B 394 GLN cc_start: 0.8555 (mt0) cc_final: 0.7740 (mp10) REVERT: B 420 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5793 (tpp) REVERT: C 185 ILE cc_start: 0.9128 (mt) cc_final: 0.8865 (mm) REVERT: C 194 TYR cc_start: 0.7624 (m-80) cc_final: 0.7229 (m-80) REVERT: C 234 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8228 (mt-10) REVERT: D 162 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8062 (tpt170) REVERT: D 166 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7280 (mtt180) REVERT: D 194 TYR cc_start: 0.7529 (m-80) cc_final: 0.7233 (m-80) REVERT: D 235 TYR cc_start: 0.8736 (m-80) cc_final: 0.8386 (m-80) REVERT: D 247 PHE cc_start: 0.8735 (m-80) cc_final: 0.8500 (m-10) REVERT: D 392 PHE cc_start: 0.8804 (t80) cc_final: 0.8578 (t80) REVERT: D 393 ARG cc_start: 0.8034 (ptt-90) cc_final: 0.7736 (ptt-90) REVERT: D 420 MET cc_start: 0.6842 (tpp) cc_final: 0.6570 (tpp) REVERT: D 457 LYS cc_start: 0.8803 (pttp) cc_final: 0.8556 (pttp) REVERT: E 203 ASN cc_start: 0.8874 (m-40) cc_final: 0.8368 (m110) REVERT: E 234 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8016 (mt-10) REVERT: E 235 TYR cc_start: 0.8707 (m-80) cc_final: 0.8352 (m-80) REVERT: E 394 GLN cc_start: 0.8569 (mt0) cc_final: 0.7929 (mp10) REVERT: E 402 TYR cc_start: 0.8671 (t80) cc_final: 0.8167 (t80) REVERT: E 420 MET cc_start: 0.5601 (tpp) cc_final: 0.5376 (tpp) REVERT: F 191 ILE cc_start: 0.7950 (mp) cc_final: 0.7695 (mt) REVERT: F 194 TYR cc_start: 0.7571 (m-80) cc_final: 0.7206 (m-80) REVERT: F 234 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8071 (mt-10) REVERT: F 372 PRO cc_start: 0.9161 (Cg_endo) cc_final: 0.8862 (Cg_exo) REVERT: F 435 ASP cc_start: 0.7661 (t0) cc_final: 0.6709 (t0) REVERT: F 457 LYS cc_start: 0.8842 (pttp) cc_final: 0.8605 (pttp) REVERT: F 458 MET cc_start: 0.7116 (tmm) cc_final: 0.6657 (tmm) REVERT: F 469 GLU cc_start: 0.7553 (tt0) cc_final: 0.7167 (tm-30) outliers start: 73 outliers final: 55 residues processed: 635 average time/residue: 0.1651 time to fit residues: 164.2376 Evaluate side-chains 601 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 544 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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 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 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 47 THR 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 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 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 216 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN A 429 HIS ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 ASN F 308 ASN ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.112554 restraints weight = 39798.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116085 restraints weight = 22766.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118448 restraints weight = 15745.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120056 restraints weight = 12286.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121169 restraints weight = 10375.322| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 23454 Z= 0.409 Angle : 0.833 9.359 31683 Z= 0.429 Chirality : 0.052 0.165 3534 Planarity : 0.006 0.045 4062 Dihedral : 11.217 107.713 3456 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.40 % Allowed : 18.02 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 2880 helix: 0.67 (0.16), residues: 1050 sheet: -0.31 (0.18), residues: 744 loop : -0.80 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 257 TYR 0.036 0.003 TYR F 402 PHE 0.028 0.003 PHE F 315 TRP 0.018 0.002 TRP C 331 HIS 0.017 0.004 HIS C 429 Details of bonding type rmsd covalent geometry : bond 0.00944 (23448) covalent geometry : angle 0.83337 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.04317 ( 1134) hydrogen bonds : angle 5.32252 ( 3060) Misc. bond : bond 0.00041 ( 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 667 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 560 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8840 (m-80) cc_final: 0.8324 (m-80) REVERT: A 352 GLU cc_start: 0.8700 (mp0) cc_final: 0.8490 (mp0) REVERT: A 361 GLN cc_start: 0.9191 (tp40) cc_final: 0.8969 (tp40) REVERT: A 385 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7633 (ttm170) REVERT: A 393 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7829 (ptt-90) REVERT: B 170 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7823 (mtm180) REVERT: B 234 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 235 TYR cc_start: 0.8741 (m-80) cc_final: 0.8352 (m-80) REVERT: B 394 GLN cc_start: 0.8602 (mt0) cc_final: 0.8045 (mp10) REVERT: C 170 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7885 (mtm180) REVERT: C 194 TYR cc_start: 0.7684 (m-80) cc_final: 0.7272 (m-80) REVERT: C 234 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8160 (mt-10) REVERT: C 457 LYS cc_start: 0.9047 (pttp) cc_final: 0.8722 (pttp) REVERT: D 86 ASN cc_start: 0.8511 (m-40) cc_final: 0.8311 (m-40) REVERT: D 162 ARG cc_start: 0.8529 (mmm160) cc_final: 0.8039 (tmt-80) REVERT: D 166 ARG cc_start: 0.8060 (mtm180) cc_final: 0.7555 (mtm180) REVERT: D 235 TYR cc_start: 0.8813 (m-80) cc_final: 0.8461 (m-80) REVERT: D 352 GLU cc_start: 0.8671 (mp0) cc_final: 0.8464 (mp0) REVERT: D 385 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7427 (ttm170) REVERT: D 393 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7826 (ptt-90) REVERT: E 170 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7624 (mtm180) REVERT: E 234 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7861 (mt-10) REVERT: E 235 TYR cc_start: 0.8740 (m-80) cc_final: 0.8344 (m-80) REVERT: E 345 LYS cc_start: 0.8760 (mtpp) cc_final: 0.7874 (ttpt) REVERT: E 348 CYS cc_start: 0.8818 (m) cc_final: 0.8438 (m) REVERT: F 106 LEU cc_start: 0.8734 (tt) cc_final: 0.8528 (tt) REVERT: F 166 ARG cc_start: 0.8294 (mtt90) cc_final: 0.8003 (mmt90) REVERT: F 170 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7896 (mtm180) REVERT: F 194 TYR cc_start: 0.7688 (m-80) cc_final: 0.7371 (m-80) REVERT: F 234 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8104 (mt-10) REVERT: F 372 PRO cc_start: 0.9268 (Cg_endo) cc_final: 0.9007 (Cg_exo) REVERT: F 458 MET cc_start: 0.7445 (tmm) cc_final: 0.7127 (tmm) outliers start: 107 outliers final: 88 residues processed: 619 average time/residue: 0.1625 time to fit residues: 158.3848 Evaluate side-chains 610 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 520 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 429 HIS 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 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU 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 204 VAL Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 324 LEU 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 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 409 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 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 222 ILE Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 278 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 126 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 263 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS E 304 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119088 restraints weight = 38495.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122847 restraints weight = 21622.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125438 restraints weight = 14654.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127069 restraints weight = 11240.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128271 restraints weight = 9429.498| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5544 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= 0.136 Angle : 0.641 8.302 31683 Z= 0.325 Chirality : 0.045 0.190 3534 Planarity : 0.004 0.042 4062 Dihedral : 10.326 112.312 3456 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.67 % Allowed : 20.91 % Favored : 76.42 % 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: 0.23 (0.16), residues: 2880 helix: 1.12 (0.16), residues: 1050 sheet: -0.17 (0.20), residues: 678 loop : -0.41 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 216 TYR 0.033 0.002 TYR C 402 PHE 0.018 0.002 PHE E 59 TRP 0.014 0.002 TRP C 331 HIS 0.023 0.003 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00305 (23448) covalent geometry : angle 0.64086 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.03213 ( 1134) hydrogen bonds : angle 4.68626 ( 3060) Misc. bond : bond 0.00033 ( 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 678 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 613 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8778 (mmt180) cc_final: 0.8421 (mmt90) REVERT: A 235 TYR cc_start: 0.8688 (m-80) cc_final: 0.8146 (m-80) REVERT: A 247 PHE cc_start: 0.8705 (m-80) cc_final: 0.8493 (m-10) REVERT: A 385 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7711 (ttm170) REVERT: A 393 ARG cc_start: 0.8001 (ptt-90) cc_final: 0.7765 (ptt-90) REVERT: A 469 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 170 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7708 (mtm180) REVERT: B 203 ASN cc_start: 0.8752 (m-40) cc_final: 0.8247 (m-40) REVERT: B 216 ARG cc_start: 0.8890 (mmt180) cc_final: 0.8558 (mmt90) REVERT: B 234 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 235 TYR cc_start: 0.8731 (m-80) cc_final: 0.8266 (m-80) REVERT: B 247 PHE cc_start: 0.8763 (m-80) cc_final: 0.8561 (m-10) REVERT: B 394 GLN cc_start: 0.8380 (mt0) cc_final: 0.7905 (mp10) REVERT: B 420 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5940 (tpp) REVERT: C 194 TYR cc_start: 0.7569 (m-80) cc_final: 0.7269 (m-80) REVERT: C 221 GLU cc_start: 0.7341 (tt0) cc_final: 0.6969 (tt0) REVERT: C 234 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8229 (mt-10) REVERT: C 372 PRO cc_start: 0.9172 (Cg_endo) cc_final: 0.8894 (Cg_exo) REVERT: D 162 ARG cc_start: 0.8328 (mmm160) cc_final: 0.8052 (tpt170) REVERT: D 166 ARG cc_start: 0.7933 (mtm180) cc_final: 0.7256 (mtt180) REVERT: D 194 TYR cc_start: 0.7608 (m-80) cc_final: 0.7293 (m-80) REVERT: D 235 TYR cc_start: 0.8708 (m-80) cc_final: 0.8320 (m-80) REVERT: D 385 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7525 (ttm170) REVERT: D 393 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7750 (ptt-90) REVERT: D 469 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7093 (tm-30) REVERT: E 170 ARG cc_start: 0.8001 (mtm-85) cc_final: 0.7662 (mtm180) REVERT: E 234 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7851 (mt-10) REVERT: E 235 TYR cc_start: 0.8736 (m-80) cc_final: 0.8237 (m-80) REVERT: E 304 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8532 (t0) REVERT: E 345 LYS cc_start: 0.8674 (mtpp) cc_final: 0.7841 (ttpt) REVERT: E 420 MET cc_start: 0.6076 (tpp) cc_final: 0.5691 (tpp) REVERT: E 435 ASP cc_start: 0.7669 (t0) cc_final: 0.7455 (t0) REVERT: E 457 LYS cc_start: 0.8731 (pttp) cc_final: 0.8489 (pttp) REVERT: F 166 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7863 (mmt90) REVERT: F 194 TYR cc_start: 0.7494 (m-80) cc_final: 0.7169 (m-80) REVERT: F 234 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8235 (mt-10) REVERT: F 372 PRO cc_start: 0.9194 (Cg_endo) cc_final: 0.8912 (Cg_exo) REVERT: F 458 MET cc_start: 0.7195 (tmm) cc_final: 0.6892 (tmm) outliers start: 65 outliers final: 50 residues processed: 651 average time/residue: 0.1647 time to fit residues: 169.4380 Evaluate side-chains 605 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 553 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 429 HIS 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 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 409 THR Chi-restraints excluded: chain B residue 420 MET 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 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 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 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 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain 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 167 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 228 optimal weight: 0.9990 chunk 255 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS E 304 ASN F 131 ASN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** 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 = 0.3717 r_free = 0.3717 target = 0.148887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118682 restraints weight = 38508.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122411 restraints weight = 21637.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124824 restraints weight = 14677.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126545 restraints weight = 11379.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127695 restraints weight = 9520.848| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23454 Z= 0.158 Angle : 0.647 9.584 31683 Z= 0.325 Chirality : 0.046 0.175 3534 Planarity : 0.004 0.042 4062 Dihedral : 10.052 112.492 3456 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.80 % Allowed : 22.26 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.16), residues: 2880 helix: 1.17 (0.16), residues: 1050 sheet: -0.27 (0.20), residues: 702 loop : -0.35 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 385 TYR 0.032 0.002 TYR F 402 PHE 0.036 0.002 PHE F 392 TRP 0.011 0.001 TRP F 92 HIS 0.017 0.002 HIS E 429 Details of bonding type rmsd covalent geometry : bond 0.00364 (23448) covalent geometry : angle 0.64693 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.03135 ( 1134) hydrogen bonds : angle 4.70146 ( 3060) Misc. bond : bond 0.00029 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 575 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8697 (m-80) cc_final: 0.8221 (m-80) REVERT: A 469 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7275 (tm-30) REVERT: B 170 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7665 (mtm180) REVERT: B 216 ARG cc_start: 0.8866 (mmt180) cc_final: 0.8531 (mmt90) REVERT: B 234 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 235 TYR cc_start: 0.8783 (m-80) cc_final: 0.8277 (m-80) REVERT: B 247 PHE cc_start: 0.8659 (m-80) cc_final: 0.8406 (m-10) REVERT: B 394 GLN cc_start: 0.8414 (mt0) cc_final: 0.7900 (mp10) REVERT: C 21 MET cc_start: 0.8131 (ptp) cc_final: 0.7902 (ptm) REVERT: C 185 ILE cc_start: 0.9150 (mt) cc_final: 0.8887 (mm) REVERT: C 187 GLU cc_start: 0.6818 (mp0) cc_final: 0.6447 (mp0) REVERT: C 194 TYR cc_start: 0.7472 (m-80) cc_final: 0.7173 (m-80) REVERT: C 221 GLU cc_start: 0.7356 (tt0) cc_final: 0.6953 (tt0) REVERT: C 234 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8191 (mt-10) REVERT: C 372 PRO cc_start: 0.9159 (Cg_endo) cc_final: 0.8888 (Cg_exo) REVERT: C 418 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7959 (mm-40) REVERT: C 443 VAL cc_start: 0.7794 (t) cc_final: 0.7448 (m) REVERT: D 162 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7910 (tpt90) REVERT: D 166 ARG cc_start: 0.7911 (mtm180) cc_final: 0.7367 (mtt180) REVERT: D 194 TYR cc_start: 0.7631 (m-80) cc_final: 0.7350 (m-80) REVERT: D 235 TYR cc_start: 0.8751 (m-80) cc_final: 0.8352 (m-80) REVERT: D 443 VAL cc_start: 0.7797 (t) cc_final: 0.7506 (m) REVERT: D 469 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7308 (tm-30) REVERT: E 170 ARG cc_start: 0.7962 (mtm-85) cc_final: 0.7663 (mtm180) REVERT: E 187 GLU cc_start: 0.6799 (mp0) cc_final: 0.6532 (mp0) REVERT: E 234 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7845 (mt-10) REVERT: E 235 TYR cc_start: 0.8804 (m-80) cc_final: 0.8271 (m-80) REVERT: E 435 ASP cc_start: 0.7665 (t0) cc_final: 0.7403 (t0) REVERT: F 166 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7874 (mmt90) REVERT: F 194 TYR cc_start: 0.7456 (m-80) cc_final: 0.7162 (m-80) REVERT: F 234 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8164 (mt-10) REVERT: F 247 PHE cc_start: 0.8394 (m-80) cc_final: 0.8107 (m-80) REVERT: F 372 PRO cc_start: 0.9167 (Cg_endo) cc_final: 0.8883 (Cg_exo) REVERT: F 443 VAL cc_start: 0.7883 (t) cc_final: 0.7565 (m) REVERT: F 458 MET cc_start: 0.7263 (tmm) cc_final: 0.6934 (tmm) outliers start: 68 outliers final: 55 residues processed: 614 average time/residue: 0.1642 time to fit residues: 160.0817 Evaluate side-chains 607 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 552 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 272 GLU Chi-restraints excluded: chain B residue 290 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 C residue 47 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU 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 319 GLU Chi-restraints excluded: chain D residue 365 SER 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 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain 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 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 436 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 164 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 95 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS E 304 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 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 = 0.147738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117300 restraints weight = 39012.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120979 restraints weight = 22027.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123461 restraints weight = 15040.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125144 restraints weight = 11628.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126159 restraints weight = 9755.423| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23454 Z= 0.192 Angle : 0.655 8.748 31683 Z= 0.332 Chirality : 0.046 0.193 3534 Planarity : 0.004 0.041 4062 Dihedral : 9.930 112.782 3456 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.51 % Allowed : 22.76 % Favored : 74.73 % 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: 0.20 (0.16), residues: 2880 helix: 1.15 (0.16), residues: 1050 sheet: -0.29 (0.20), residues: 702 loop : -0.43 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 138 TYR 0.034 0.002 TYR F 402 PHE 0.028 0.002 PHE B 392 TRP 0.011 0.001 TRP F 92 HIS 0.018 0.003 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00442 (23448) covalent geometry : angle 0.65552 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.03202 ( 1134) hydrogen bonds : angle 4.74425 ( 3060) Misc. bond : bond 0.00018 ( 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 624 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 563 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8711 (m-80) cc_final: 0.8236 (m-80) REVERT: A 385 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7822 (ttm170) REVERT: A 450 SER cc_start: 0.8593 (m) cc_final: 0.8120 (p) REVERT: B 170 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7663 (mtm180) REVERT: B 216 ARG cc_start: 0.8879 (mmt180) cc_final: 0.8540 (mmt90) REVERT: B 234 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 235 TYR cc_start: 0.8806 (m-80) cc_final: 0.8337 (m-80) REVERT: B 247 PHE cc_start: 0.8723 (m-80) cc_final: 0.8441 (m-10) REVERT: B 394 GLN cc_start: 0.8453 (mt0) cc_final: 0.7970 (mp10) REVERT: C 21 MET cc_start: 0.8151 (ptp) cc_final: 0.7940 (ptm) REVERT: C 185 ILE cc_start: 0.9210 (mt) cc_final: 0.8936 (mm) REVERT: C 187 GLU cc_start: 0.6887 (mp0) cc_final: 0.6509 (mp0) REVERT: C 194 TYR cc_start: 0.7529 (m-80) cc_final: 0.7224 (m-80) REVERT: C 221 GLU cc_start: 0.7393 (tt0) cc_final: 0.6976 (tt0) REVERT: C 234 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8156 (mt-10) REVERT: C 372 PRO cc_start: 0.9172 (Cg_endo) cc_final: 0.8886 (Cg_exo) REVERT: C 418 GLN cc_start: 0.8249 (mm-40) cc_final: 0.8015 (mm-40) REVERT: D 162 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7913 (tpt170) REVERT: D 181 THR cc_start: 0.9043 (m) cc_final: 0.8731 (m) REVERT: D 235 TYR cc_start: 0.8754 (m-80) cc_final: 0.8369 (m-80) REVERT: D 361 GLN cc_start: 0.9219 (tp40) cc_final: 0.8919 (tp40) REVERT: D 443 VAL cc_start: 0.7821 (t) cc_final: 0.7529 (m) REVERT: D 469 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7219 (tm-30) REVERT: E 170 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7669 (mtm180) REVERT: E 187 GLU cc_start: 0.6795 (mp0) cc_final: 0.6427 (mp0) REVERT: E 188 TYR cc_start: 0.8576 (m-80) cc_final: 0.8345 (m-10) REVERT: E 234 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7894 (mt-10) REVERT: E 235 TYR cc_start: 0.8820 (m-80) cc_final: 0.8286 (m-80) REVERT: E 304 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8397 (t0) REVERT: E 345 LYS cc_start: 0.8651 (mtpp) cc_final: 0.7807 (ttpt) REVERT: E 394 GLN cc_start: 0.8417 (mt0) cc_final: 0.7926 (mp10) REVERT: E 420 MET cc_start: 0.6007 (tpp) cc_final: 0.5741 (tpp) REVERT: E 443 VAL cc_start: 0.7716 (t) cc_final: 0.7453 (m) REVERT: F 166 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7763 (mmt90) REVERT: F 194 TYR cc_start: 0.7563 (m-80) cc_final: 0.7269 (m-80) REVERT: F 234 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8171 (mt-10) REVERT: F 372 PRO cc_start: 0.9199 (Cg_endo) cc_final: 0.8914 (Cg_exo) REVERT: F 435 ASP cc_start: 0.7973 (t0) cc_final: 0.7711 (t0) REVERT: F 458 MET cc_start: 0.7276 (tmm) cc_final: 0.6935 (tmm) outliers start: 61 outliers final: 57 residues processed: 601 average time/residue: 0.1590 time to fit residues: 152.0574 Evaluate side-chains 605 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 547 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 415 THR 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 365 SER 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 180 MET Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 304 ASN Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 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 436 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 261 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 263 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 136 optimal weight: 0.0980 chunk 285 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS E 304 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 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 = 0.3724 r_free = 0.3724 target = 0.149358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119183 restraints weight = 38634.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122879 restraints weight = 21786.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125356 restraints weight = 14854.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.127061 restraints weight = 11450.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128004 restraints weight = 9587.648| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23454 Z= 0.150 Angle : 0.643 8.713 31683 Z= 0.325 Chirality : 0.046 0.172 3534 Planarity : 0.004 0.052 4062 Dihedral : 9.724 113.636 3456 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.06 % Allowed : 23.66 % Favored : 74.28 % 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: 1.19 (0.16), residues: 1050 sheet: -0.27 (0.19), residues: 756 loop : -0.50 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 385 TYR 0.034 0.002 TYR C 402 PHE 0.029 0.002 PHE E 392 TRP 0.011 0.001 TRP F 92 HIS 0.018 0.002 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00340 (23448) covalent geometry : angle 0.64274 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.03059 ( 1134) hydrogen bonds : angle 4.64679 ( 3060) Misc. bond : bond 0.00023 ( 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 624 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 574 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 THR cc_start: 0.8969 (m) cc_final: 0.8637 (m) REVERT: A 235 TYR cc_start: 0.8698 (m-80) cc_final: 0.8221 (m-80) REVERT: A 366 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7958 (tp30) REVERT: A 385 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7750 (ttm170) REVERT: A 419 PHE cc_start: 0.7580 (m-80) cc_final: 0.7363 (m-80) REVERT: A 450 SER cc_start: 0.8457 (m) cc_final: 0.8057 (p) REVERT: A 469 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 170 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7719 (mtm180) REVERT: B 187 GLU cc_start: 0.6765 (mp0) cc_final: 0.6545 (mp0) REVERT: B 216 ARG cc_start: 0.8825 (mmt180) cc_final: 0.8491 (mmt90) REVERT: B 234 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 235 TYR cc_start: 0.8775 (m-80) cc_final: 0.8306 (m-80) REVERT: B 247 PHE cc_start: 0.8652 (m-80) cc_final: 0.8363 (m-10) REVERT: B 394 GLN cc_start: 0.8443 (mt0) cc_final: 0.7916 (mp10) REVERT: B 469 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 185 ILE cc_start: 0.9182 (mt) cc_final: 0.8915 (mm) REVERT: C 187 GLU cc_start: 0.6854 (mp0) cc_final: 0.6515 (mp0) REVERT: C 194 TYR cc_start: 0.7520 (m-80) cc_final: 0.7246 (m-80) REVERT: C 221 GLU cc_start: 0.7383 (tt0) cc_final: 0.6941 (tt0) REVERT: C 234 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8159 (mt-10) REVERT: C 372 PRO cc_start: 0.9161 (Cg_endo) cc_final: 0.8882 (Cg_exo) REVERT: C 418 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8115 (mm-40) REVERT: D 162 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7899 (tpt170) REVERT: D 181 THR cc_start: 0.8987 (m) cc_final: 0.8662 (m) REVERT: D 235 TYR cc_start: 0.8720 (m-80) cc_final: 0.8343 (m-80) REVERT: D 247 PHE cc_start: 0.8755 (m-80) cc_final: 0.8402 (m-10) REVERT: D 361 GLN cc_start: 0.9230 (tp40) cc_final: 0.8955 (tp40) REVERT: D 469 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7228 (tm-30) REVERT: E 170 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7653 (mtm180) REVERT: E 187 GLU cc_start: 0.6706 (mp0) cc_final: 0.6339 (mp0) REVERT: E 188 TYR cc_start: 0.8530 (m-80) cc_final: 0.8295 (m-10) REVERT: E 234 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7798 (mt-10) REVERT: E 235 TYR cc_start: 0.8786 (m-80) cc_final: 0.8239 (m-80) REVERT: E 345 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7835 (ttpt) REVERT: E 394 GLN cc_start: 0.8465 (mt0) cc_final: 0.8038 (mp10) REVERT: E 443 VAL cc_start: 0.7699 (t) cc_final: 0.7425 (m) REVERT: E 450 SER cc_start: 0.8082 (m) cc_final: 0.7757 (p) REVERT: F 166 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7714 (mmt90) REVERT: F 187 GLU cc_start: 0.6966 (mp0) cc_final: 0.6661 (mp0) REVERT: F 194 TYR cc_start: 0.7506 (m-80) cc_final: 0.7242 (m-80) REVERT: F 234 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8182 (mt-10) REVERT: F 372 PRO cc_start: 0.9193 (Cg_endo) cc_final: 0.8899 (Cg_exo) REVERT: F 435 ASP cc_start: 0.7933 (t0) cc_final: 0.7669 (t0) REVERT: F 458 MET cc_start: 0.7229 (tmm) cc_final: 0.6891 (tmm) outliers start: 50 outliers final: 46 residues processed: 603 average time/residue: 0.1609 time to fit residues: 154.3926 Evaluate side-chains 602 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 556 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 290 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 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 127 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain 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 290 THR 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: 2.9990 chunk 287 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 199 optimal weight: 0.7980 chunk 170 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 ASN ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 HIS ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3735 r_free = 0.3735 target = 0.150164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119926 restraints weight = 38438.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.123632 restraints weight = 21680.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126040 restraints weight = 14790.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127731 restraints weight = 11464.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128721 restraints weight = 9666.981| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23454 Z= 0.141 Angle : 0.634 8.691 31683 Z= 0.320 Chirality : 0.046 0.180 3534 Planarity : 0.004 0.047 4062 Dihedral : 9.563 115.052 3456 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.02 % Allowed : 24.28 % Favored : 73.70 % 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 (0.16), residues: 2880 helix: 1.28 (0.16), residues: 1050 sheet: -0.24 (0.19), residues: 756 loop : -0.51 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 385 TYR 0.032 0.001 TYR C 402 PHE 0.031 0.002 PHE D 392 TRP 0.011 0.001 TRP F 92 HIS 0.017 0.002 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00322 (23448) covalent geometry : angle 0.63364 (31680) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.02982 ( 1134) hydrogen bonds : angle 4.59252 ( 3060) Misc. bond : bond 0.00023 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4391.18 seconds wall clock time: 76 minutes 37.69 seconds (4597.69 seconds total)