Starting phenix.real_space_refine on Sun Sep 29 16:11:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/09_2024/7s67_24852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/09_2024/7s67_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/09_2024/7s67_24852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/09_2024/7s67_24852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/09_2024/7s67_24852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s67_24852/09_2024/7s67_24852.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'PHE:plan': 1, 'GLU: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: {'PHE:plan': 1, 'GLU: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: 12.05, per 1000 atoms: 0.52 Number of scatterers: 23058 At special positions: 0 Unit cell: (118.45, 118.45, 109.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 30 15.00 Mg 12 11.99 O 4440 8.00 N 4056 7.00 C 14430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.8 seconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 41.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 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: 8.24 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4061 1.31 - 1.44: 5983 1.44 - 1.56: 13200 1.56 - 1.69: 42 1.69 - 1.81: 162 Bond restraints: 23448 Sorted by residual: bond pdb=" C4 ADP F 602 " pdb=" C5 ADP F 602 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C4 ADP D 603 " pdb=" C5 ADP D 603 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 ADP C 603 " pdb=" C5 ADP C 603 " ideal model delta sigma weight residual 1.490 1.347 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" C4 ADP A 603 " pdb=" C5 ADP A 603 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 23443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 31181 4.26 - 8.51: 469 8.51 - 12.77: 12 12.77 - 17.03: 0 17.03 - 21.28: 18 Bond angle restraints: 31680 Sorted by residual: angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 116.10 20.73 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 116.11 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 116.11 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP D 601 " pdb=" O3A ATP D 601 " pdb=" PB ATP D 601 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 ... (remaining 31675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.18: 13864 29.18 - 58.36: 272 58.36 - 87.54: 42 87.54 - 116.72: 6 116.72 - 145.90: 6 Dihedral angle restraints: 14190 sinusoidal: 5928 harmonic: 8262 Sorted by residual: dihedral pdb=" C5' ADP B 603 " pdb=" O5' ADP B 603 " pdb=" PA ADP B 603 " pdb=" O2A ADP B 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.10 145.90 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP E 902 " pdb=" O5' ADP E 902 " pdb=" PA ADP E 902 " pdb=" O2A ADP E 902 " ideal model delta sinusoidal sigma weight residual 300.00 154.15 145.85 1 2.00e+01 2.50e-03 4.39e+01 dihedral pdb=" C5' ADP A 603 " pdb=" O5' ADP A 603 " pdb=" PA ADP A 603 " pdb=" O2A ADP A 603 " ideal model delta sinusoidal sigma weight residual 300.00 154.15 145.85 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 14187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2513 0.064 - 0.128: 813 0.128 - 0.191: 176 0.191 - 0.255: 20 0.255 - 0.319: 12 Chirality restraints: 3534 Sorted by residual: chirality pdb=" CA HIS D 429 " pdb=" N HIS D 429 " pdb=" C HIS D 429 " pdb=" CB HIS D 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA HIS A 429 " pdb=" N HIS A 429 " pdb=" C HIS A 429 " pdb=" CB HIS A 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA HIS E 429 " pdb=" N HIS E 429 " pdb=" C HIS E 429 " pdb=" CB HIS E 429 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 3531 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP C 603 " -0.175 2.00e-02 2.50e+03 7.17e-02 1.41e+02 pdb=" C2 ADP C 603 " 0.024 2.00e-02 2.50e+03 pdb=" C4 ADP C 603 " 0.065 2.00e-02 2.50e+03 pdb=" C5 ADP C 603 " 0.028 2.00e-02 2.50e+03 pdb=" C6 ADP C 603 " -0.016 2.00e-02 2.50e+03 pdb=" C8 ADP C 603 " 0.066 2.00e-02 2.50e+03 pdb=" N1 ADP C 603 " -0.029 2.00e-02 2.50e+03 pdb=" N3 ADP C 603 " 0.063 2.00e-02 2.50e+03 pdb=" N6 ADP C 603 " -0.092 2.00e-02 2.50e+03 pdb=" N7 ADP C 603 " 0.023 2.00e-02 2.50e+03 pdb=" N9 ADP C 603 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP E 902 " 0.175 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" C2 ADP E 902 " -0.024 2.00e-02 2.50e+03 pdb=" C4 ADP E 902 " -0.065 2.00e-02 2.50e+03 pdb=" C5 ADP E 902 " -0.028 2.00e-02 2.50e+03 pdb=" C6 ADP E 902 " 0.016 2.00e-02 2.50e+03 pdb=" C8 ADP E 902 " -0.066 2.00e-02 2.50e+03 pdb=" N1 ADP E 902 " 0.028 2.00e-02 2.50e+03 pdb=" N3 ADP E 902 " -0.063 2.00e-02 2.50e+03 pdb=" N6 ADP E 902 " 0.092 2.00e-02 2.50e+03 pdb=" N7 ADP E 902 " -0.023 2.00e-02 2.50e+03 pdb=" N9 ADP E 902 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 603 " -0.175 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" C2 ADP B 603 " 0.024 2.00e-02 2.50e+03 pdb=" C4 ADP B 603 " 0.064 2.00e-02 2.50e+03 pdb=" C5 ADP B 603 " 0.028 2.00e-02 2.50e+03 pdb=" C6 ADP B 603 " -0.016 2.00e-02 2.50e+03 pdb=" C8 ADP B 603 " 0.066 2.00e-02 2.50e+03 pdb=" N1 ADP B 603 " -0.029 2.00e-02 2.50e+03 pdb=" N3 ADP B 603 " 0.063 2.00e-02 2.50e+03 pdb=" N6 ADP B 603 " -0.092 2.00e-02 2.50e+03 pdb=" N7 ADP B 603 " 0.023 2.00e-02 2.50e+03 pdb=" N9 ADP B 603 " 0.043 2.00e-02 2.50e+03 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 64 2.43 - 3.05: 15207 3.05 - 3.67: 34459 3.67 - 4.28: 56802 4.28 - 4.90: 89877 Nonbonded interactions: 196409 Sorted by model distance: nonbonded pdb=" NH1 ARG F 226 " pdb=" O2G ATP F 601 " model vdw 1.815 3.120 nonbonded pdb=" NH1 ARG C 226 " pdb=" O2G ATP B 601 " model vdw 1.887 3.120 nonbonded pdb=" NH1 ARG E 226 " pdb=" O2G ATP D 601 " model vdw 1.912 3.120 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 1.917 2.170 nonbonded pdb=" O2G ATP A 605 " pdb="MG MG A 606 " model vdw 1.918 2.170 ... (remaining 196404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 16 through 497) selection = (chain 'B' and resid 16 through 497) selection = (chain 'C' and resid 16 through 497) selection = (chain 'D' and resid 16 through 497) selection = (chain 'E' and resid 16 through 497) selection = (chain 'F' and resid 16 through 497) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 49.440 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.060 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.100 ------------------------------------------------------------------------------- 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 : 0.013 0.143 23448 Z= 0.859 Angle : 1.395 21.283 31680 Z= 0.953 Chirality : 0.067 0.319 3534 Planarity : 0.011 0.072 4062 Dihedral : 12.758 145.899 8886 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (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 TRP 0.066 0.018 TRP E 92 HIS 0.009 0.003 HIS F 423 PHE 0.037 0.008 PHE E 237 TYR 0.109 0.015 TYR D 442 ARG 0.011 0.001 ARG C 451 *********************** 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 fitting. rotamer outliers: 0 poor density : 1032 time to evaluate : 2.476 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: 0.6775 (m-30) REVERT: A 234 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7822 (mt-10) REVERT: A 235 TYR cc_start: 0.8591 (m-80) cc_final: 0.8121 (m-80) REVERT: A 247 PHE cc_start: 0.8559 (m-80) cc_final: 0.8331 (m-10) REVERT: A 442 TYR cc_start: 0.6837 (m-80) cc_final: 0.6562 (m-80) REVERT: B 82 ASP cc_start: 0.7607 (m-30) cc_final: 0.7201 (m-30) REVERT: B 234 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 235 TYR cc_start: 0.8637 (m-80) cc_final: 0.8246 (m-80) REVERT: B 247 PHE cc_start: 0.8546 (m-80) cc_final: 0.8275 (m-10) REVERT: B 357 GLU cc_start: 0.8395 (mp0) cc_final: 0.8018 (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: 0.8335 (m-10) REVERT: C 357 GLU cc_start: 0.8516 (mp0) cc_final: 0.8194 (mp0) REVERT: D 82 ASP cc_start: 0.7021 (m-30) cc_final: 0.6820 (m-30) 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: 0.8249 (mp0) REVERT: D 442 TYR cc_start: 0.6727 (m-80) cc_final: 0.6490 (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: 0.8128 (m-80) REVERT: E 234 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7534 (mt-10) REVERT: E 235 TYR cc_start: 0.8673 (m-80) cc_final: 0.8276 (m-80) REVERT: E 247 PHE cc_start: 0.8608 (m-80) cc_final: 0.8219 (m-10) REVERT: E 357 GLU cc_start: 0.8517 (mp0) cc_final: 0.8194 (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: 0.7922 (mt-10) REVERT: F 247 PHE cc_start: 0.8586 (m-80) cc_final: 0.8320 (m-10) REVERT: F 357 GLU cc_start: 0.8448 (mp0) cc_final: 0.8143 (mp0) outliers start: 0 outliers final: 0 residues processed: 1032 average time/residue: 0.4202 time to fit residues: 629.9626 Evaluate side-chains 580 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 260 ASN B 341 GLN B 342 ASN B 423 HIS ** 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 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23448 Z= 0.228 Angle : 0.664 7.443 31680 Z= 0.350 Chirality : 0.047 0.165 3534 Planarity : 0.005 0.051 4062 Dihedral : 11.895 122.627 3456 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.93 % Allowed : 12.14 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 2880 helix: 0.51 (0.15), residues: 1050 sheet: 0.45 (0.20), residues: 714 loop : 0.36 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 331 HIS 0.019 0.003 HIS C 429 PHE 0.023 0.002 PHE A 419 TYR 0.024 0.002 TYR C 442 ARG 0.006 0.001 ARG E 217 *********************** 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 731 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 684 time to evaluate : 2.300 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: symmetry clash REVERT: A 24 MET cc_start: 0.6940 (mmt) cc_final: 0.6737 (mmt) REVERT: A 76 PHE cc_start: 0.7785 (m-80) cc_final: 0.7438 (m-10) REVERT: A 234 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 235 TYR cc_start: 0.8545 (m-80) cc_final: 0.8052 (m-80) REVERT: A 420 MET cc_start: 0.5518 (tpp) cc_final: 0.5169 (tpp) REVERT: B 132 TYR cc_start: 0.6154 (t80) cc_final: 0.5768 (t80) REVERT: B 234 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 235 TYR cc_start: 0.8555 (m-80) cc_final: 0.8139 (m-80) REVERT: B 247 PHE cc_start: 0.8394 (m-80) cc_final: 0.8119 (m-10) REVERT: B 358 ASP cc_start: 0.6880 (m-30) cc_final: 0.6649 (m-30) REVERT: B 394 GLN cc_start: 0.7788 (mt0) cc_final: 0.7500 (mp10) REVERT: C 86 ASN cc_start: 0.8343 (m-40) cc_final: 0.8111 (m-40) REVERT: C 216 ARG cc_start: 0.8612 (mmt180) cc_final: 0.8410 (mmt90) REVERT: C 273 MET cc_start: 0.6502 (mtp) cc_final: 0.6164 (mtp) REVERT: C 420 MET cc_start: 0.5786 (tpp) cc_final: 0.5426 (tpp) REVERT: D 127 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7778 (pt) REVERT: D 166 ARG cc_start: 0.7513 (mtm180) cc_final: 0.6879 (mtt180) REVERT: D 234 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7675 (mt-10) REVERT: D 235 TYR cc_start: 0.8544 (m-80) cc_final: 0.8168 (m-80) REVERT: D 393 ARG cc_start: 0.7326 (ptt-90) cc_final: 0.7087 (ptt-90) REVERT: D 420 MET cc_start: 0.5788 (tpp) cc_final: 0.5509 (tpp) REVERT: E 132 TYR cc_start: 0.6320 (t80) cc_final: 0.6032 (t80) REVERT: E 188 TYR cc_start: 0.8245 (m-80) cc_final: 0.8027 (m-80) REVERT: E 234 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7681 (mt-10) REVERT: E 235 TYR cc_start: 0.8506 (m-80) cc_final: 0.8161 (m-80) REVERT: E 247 PHE cc_start: 0.8431 (m-80) cc_final: 0.8135 (m-10) REVERT: E 394 GLN cc_start: 0.7578 (mt0) cc_final: 0.7366 (mp10) REVERT: F 82 ASP cc_start: 0.7406 (m-30) cc_final: 0.7161 (m-30) REVERT: F 86 ASN cc_start: 0.8298 (m-40) cc_final: 0.8011 (m-40) REVERT: F 216 ARG cc_start: 0.8599 (mmt180) cc_final: 0.8399 (mmt90) REVERT: F 273 MET cc_start: 0.6438 (mtp) cc_final: 0.5907 (mtp) REVERT: F 454 ASN cc_start: 0.7840 (t0) cc_final: 0.7368 (t0) outliers start: 47 outliers final: 31 residues processed: 714 average time/residue: 0.3799 time to fit residues: 419.6575 Evaluate side-chains 595 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 563 time to evaluate : 2.571 ------------------------------------------------------------------------------- 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 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 C residue 47 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 292 THR 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 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 290 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 89 optimal weight: 0.0370 chunk 210 optimal weight: 5.9990 overall best weight: 3.8064 ------------------------------------------------------------------------------- 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 327 ASN B 342 ASN ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 HIS C 463 HIS D 429 HIS E 245 ASN E 304 ASN E 429 HIS F 203 ASN F 304 ASN F 308 ASN F 323 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23448 Z= 0.339 Angle : 0.678 10.839 31680 Z= 0.349 Chirality : 0.047 0.165 3534 Planarity : 0.005 0.045 4062 Dihedral : 11.785 114.570 3456 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.37 % Allowed : 13.62 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2880 helix: 0.69 (0.15), residues: 1050 sheet: 0.00 (0.19), residues: 786 loop : 0.11 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 331 HIS 0.018 0.003 HIS C 429 PHE 0.028 0.002 PHE A 199 TYR 0.027 0.002 TYR D 402 ARG 0.006 0.001 ARG A 393 *********************** 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 675 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 593 time to evaluate : 2.596 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 194 TYR cc_start: 0.7211 (m-80) cc_final: 0.6922 (m-80) REVERT: A 234 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 235 TYR cc_start: 0.8675 (m-80) cc_final: 0.8093 (m-80) REVERT: A 245 ASN cc_start: 0.8059 (t0) cc_final: 0.7322 (t0) REVERT: A 302 VAL cc_start: 0.9082 (m) cc_final: 0.8777 (t) REVERT: A 420 MET cc_start: 0.5917 (tpp) cc_final: 0.5524 (tpp) REVERT: A 457 LYS cc_start: 0.7928 (pttp) cc_final: 0.7656 (pttp) REVERT: B 234 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 235 TYR cc_start: 0.8534 (m-80) cc_final: 0.8091 (m-80) REVERT: B 247 PHE cc_start: 0.8488 (m-80) cc_final: 0.8207 (m-80) REVERT: C 170 ARG cc_start: 0.7161 (mtp180) cc_final: 0.6918 (mtp85) REVERT: C 191 ILE cc_start: 0.7890 (mp) cc_final: 0.7509 (mt) REVERT: C 203 ASN cc_start: 0.8401 (m-40) cc_final: 0.7918 (m110) REVERT: C 216 ARG cc_start: 0.8595 (mmt180) cc_final: 0.8346 (mmt90) REVERT: D 166 ARG cc_start: 0.7314 (mtm180) cc_final: 0.7047 (mtt180) REVERT: D 194 TYR cc_start: 0.7074 (m-80) cc_final: 0.6768 (m-80) REVERT: D 235 TYR cc_start: 0.8683 (m-80) cc_final: 0.8238 (m-80) REVERT: D 247 PHE cc_start: 0.8125 (m-80) cc_final: 0.7598 (m-10) REVERT: D 420 MET cc_start: 0.5799 (tpp) cc_final: 0.5502 (tpp) REVERT: D 457 LYS cc_start: 0.8023 (pttp) cc_final: 0.7801 (pttp) REVERT: E 234 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7687 (mt-10) REVERT: E 235 TYR cc_start: 0.8502 (m-80) cc_final: 0.8235 (m-80) REVERT: E 245 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7793 (m-40) REVERT: E 247 PHE cc_start: 0.8465 (m-80) cc_final: 0.8177 (m-80) REVERT: E 435 ASP cc_start: 0.7132 (t0) cc_final: 0.6895 (t0) REVERT: F 86 ASN cc_start: 0.8298 (m-40) cc_final: 0.8076 (m-40) REVERT: F 194 TYR cc_start: 0.7282 (m-80) cc_final: 0.6927 (m-80) REVERT: F 216 ARG cc_start: 0.8585 (mmt180) cc_final: 0.8333 (mmt90) outliers start: 82 outliers final: 62 residues processed: 635 average time/residue: 0.3483 time to fit residues: 342.3472 Evaluate side-chains 602 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 539 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 167 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 409 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 158 SER Chi-restraints excluded: chain C residue 167 LEU 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 158 SER 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 429 HIS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 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 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 319 GLU 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 258 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 249 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 ASN ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 ASN C 308 ASN C 327 ASN C 423 HIS ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 HIS F 423 HIS ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23448 Z= 0.241 Angle : 0.618 6.955 31680 Z= 0.317 Chirality : 0.046 0.149 3534 Planarity : 0.004 0.044 4062 Dihedral : 11.555 114.219 3456 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.29 % Allowed : 15.64 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 2880 helix: 0.84 (0.16), residues: 1050 sheet: -0.08 (0.19), residues: 786 loop : 0.10 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 331 HIS 0.022 0.003 HIS A 429 PHE 0.016 0.002 PHE E 59 TYR 0.033 0.002 TYR F 402 ARG 0.005 0.000 ARG C 138 *********************** 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 669 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 589 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TYR cc_start: 0.7267 (m-80) cc_final: 0.6989 (m-80) REVERT: A 235 TYR cc_start: 0.8531 (m-80) cc_final: 0.7931 (m-80) REVERT: A 247 PHE cc_start: 0.8498 (m-80) cc_final: 0.8074 (m-10) REVERT: A 302 VAL cc_start: 0.9091 (m) cc_final: 0.8815 (t) REVERT: A 393 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7277 (ptt-90) REVERT: A 442 TYR cc_start: 0.7751 (m-80) cc_final: 0.7463 (m-80) REVERT: B 194 TYR cc_start: 0.7256 (m-80) cc_final: 0.6880 (m-80) REVERT: B 217 ARG cc_start: 0.8008 (ttt-90) cc_final: 0.7762 (ttt-90) REVERT: B 234 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 235 TYR cc_start: 0.8374 (m-80) cc_final: 0.7985 (m-80) REVERT: B 247 PHE cc_start: 0.8391 (m-80) cc_final: 0.8177 (m-80) REVERT: C 191 ILE cc_start: 0.7899 (mp) cc_final: 0.7642 (mt) REVERT: C 194 TYR cc_start: 0.7283 (m-80) cc_final: 0.6941 (m-80) REVERT: D 166 ARG cc_start: 0.7347 (mtm180) cc_final: 0.7005 (mtt-85) REVERT: D 194 TYR cc_start: 0.7284 (m-80) cc_final: 0.6938 (m-80) REVERT: D 199 PHE cc_start: 0.8630 (m-80) cc_final: 0.8283 (m-10) REVERT: D 235 TYR cc_start: 0.8617 (m-80) cc_final: 0.8153 (m-80) REVERT: D 247 PHE cc_start: 0.8434 (m-80) cc_final: 0.7932 (m-10) REVERT: D 302 VAL cc_start: 0.9058 (m) cc_final: 0.8786 (t) REVERT: D 442 TYR cc_start: 0.7825 (m-80) cc_final: 0.7503 (m-80) REVERT: E 194 TYR cc_start: 0.7191 (m-80) cc_final: 0.6849 (m-80) REVERT: E 234 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7677 (mt-10) REVERT: E 235 TYR cc_start: 0.8572 (m-80) cc_final: 0.8196 (m-80) REVERT: F 86 ASN cc_start: 0.8325 (m-40) cc_final: 0.8095 (m-40) REVERT: F 191 ILE cc_start: 0.7899 (mp) cc_final: 0.7463 (mt) REVERT: F 194 TYR cc_start: 0.7374 (m-80) cc_final: 0.7070 (m-80) REVERT: F 234 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7806 (mt-10) outliers start: 80 outliers final: 60 residues processed: 628 average time/residue: 0.3439 time to fit residues: 336.7593 Evaluate side-chains 577 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 516 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 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 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 436 THR 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 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 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 436 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN B 423 HIS ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS D 131 ASN ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 ASN ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 429 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23448 Z= 0.415 Angle : 0.703 13.262 31680 Z= 0.358 Chirality : 0.048 0.182 3534 Planarity : 0.005 0.046 4062 Dihedral : 11.348 112.789 3456 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.03 % Allowed : 16.95 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 2880 helix: 0.78 (0.16), residues: 1050 sheet: -0.13 (0.19), residues: 762 loop : -0.37 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 331 HIS 0.015 0.003 HIS E 429 PHE 0.022 0.002 PHE E 59 TYR 0.031 0.002 TYR A 402 ARG 0.006 0.001 ARG F 138 *********************** 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 665 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 567 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7256 (ttp80) REVERT: A 194 TYR cc_start: 0.7602 (m-80) cc_final: 0.7244 (m-80) REVERT: A 235 TYR cc_start: 0.8567 (m-80) cc_final: 0.7947 (m-80) REVERT: A 302 VAL cc_start: 0.9105 (m) cc_final: 0.8891 (t) REVERT: A 319 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: A 393 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7278 (ptt-90) REVERT: B 170 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7219 (mtm180) REVERT: B 217 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7852 (ttt-90) REVERT: B 234 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 235 TYR cc_start: 0.8408 (m-80) cc_final: 0.8074 (m-80) REVERT: B 302 VAL cc_start: 0.9069 (m) cc_final: 0.8735 (t) REVERT: B 402 TYR cc_start: 0.7884 (t80) cc_final: 0.7418 (t80) REVERT: C 194 TYR cc_start: 0.7609 (m-80) cc_final: 0.7187 (m-80) REVERT: C 234 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7742 (mt-10) REVERT: C 247 PHE cc_start: 0.8201 (m-80) cc_final: 0.7569 (m-10) REVERT: C 469 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7170 (tt0) REVERT: D 166 ARG cc_start: 0.7462 (mtm180) cc_final: 0.7166 (mtt-85) REVERT: D 194 TYR cc_start: 0.7493 (m-80) cc_final: 0.7124 (m-80) REVERT: D 199 PHE cc_start: 0.8672 (m-80) cc_final: 0.8425 (m-10) REVERT: D 235 TYR cc_start: 0.8643 (m-80) cc_final: 0.8135 (m-80) REVERT: D 302 VAL cc_start: 0.9091 (m) cc_final: 0.8873 (t) REVERT: E 170 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7056 (mtm180) REVERT: E 216 ARG cc_start: 0.8830 (mmt180) cc_final: 0.8627 (mmt90) REVERT: E 234 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7560 (mt-10) REVERT: E 235 TYR cc_start: 0.8578 (m-80) cc_final: 0.8094 (m-80) REVERT: E 247 PHE cc_start: 0.8562 (m-80) cc_final: 0.8321 (m-10) REVERT: E 302 VAL cc_start: 0.8950 (m) cc_final: 0.8610 (t) REVERT: E 392 PHE cc_start: 0.8580 (t80) cc_final: 0.8233 (t80) REVERT: E 402 TYR cc_start: 0.8030 (t80) cc_final: 0.7656 (t80) REVERT: F 86 ASN cc_start: 0.8241 (m-40) cc_final: 0.8019 (m-40) REVERT: F 194 TYR cc_start: 0.7453 (m-80) cc_final: 0.7124 (m-80) REVERT: F 221 GLU cc_start: 0.7557 (tt0) cc_final: 0.7041 (tt0) REVERT: F 234 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7754 (mt-10) REVERT: F 435 ASP cc_start: 0.7275 (t0) cc_final: 0.7067 (t0) outliers start: 98 outliers final: 79 residues processed: 621 average time/residue: 0.3403 time to fit residues: 330.2008 Evaluate side-chains 604 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 522 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 154 TYR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 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 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 94 LEU 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 185 ILE 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 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 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 292 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 64 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 185 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 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 278 PHE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 429 HIS Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 443 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.9990 chunk 250 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** 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 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23448 Z= 0.248 Angle : 0.634 8.953 31680 Z= 0.322 Chirality : 0.046 0.220 3534 Planarity : 0.004 0.055 4062 Dihedral : 10.827 115.098 3456 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.66 % Allowed : 18.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 2880 helix: 0.92 (0.16), residues: 1050 sheet: -0.04 (0.20), residues: 690 loop : -0.25 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 331 HIS 0.018 0.003 HIS F 429 PHE 0.023 0.002 PHE F 315 TYR 0.033 0.002 TYR A 402 ARG 0.006 0.000 ARG C 170 *********************** 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 676 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 587 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 TYR cc_start: 0.7597 (m-80) cc_final: 0.7233 (m-80) REVERT: A 235 TYR cc_start: 0.8517 (m-80) cc_final: 0.7916 (m-80) REVERT: A 393 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7208 (ptt-90) REVERT: B 234 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7624 (mt-10) REVERT: B 235 TYR cc_start: 0.8524 (m-80) cc_final: 0.8023 (m-80) REVERT: B 302 VAL cc_start: 0.9096 (m) cc_final: 0.8813 (t) REVERT: B 461 SER cc_start: 0.7832 (t) cc_final: 0.7527 (t) REVERT: C 194 TYR cc_start: 0.7520 (m-80) cc_final: 0.7177 (m-80) REVERT: C 234 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 247 PHE cc_start: 0.8305 (m-80) cc_final: 0.8038 (m-10) REVERT: C 443 VAL cc_start: 0.7392 (t) cc_final: 0.7127 (m) REVERT: C 469 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7076 (tt0) REVERT: D 194 TYR cc_start: 0.7478 (m-80) cc_final: 0.7089 (m-80) REVERT: D 235 TYR cc_start: 0.8559 (m-80) cc_final: 0.8090 (m-80) REVERT: D 247 PHE cc_start: 0.8437 (m-80) cc_final: 0.8191 (m-10) REVERT: E 203 ASN cc_start: 0.8483 (m-40) cc_final: 0.7981 (m110) REVERT: E 234 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7585 (mt-10) REVERT: E 235 TYR cc_start: 0.8463 (m-80) cc_final: 0.7982 (m-80) REVERT: E 247 PHE cc_start: 0.8601 (m-80) cc_final: 0.8377 (m-80) REVERT: E 302 VAL cc_start: 0.8945 (m) cc_final: 0.8644 (t) REVERT: E 392 PHE cc_start: 0.8586 (t80) cc_final: 0.8256 (t80) REVERT: E 402 TYR cc_start: 0.8062 (t80) cc_final: 0.7695 (t80) REVERT: F 86 ASN cc_start: 0.8278 (m-40) cc_final: 0.8037 (m-40) REVERT: F 194 TYR cc_start: 0.7407 (m-80) cc_final: 0.7146 (m-80) REVERT: F 221 GLU cc_start: 0.7549 (tt0) cc_final: 0.7111 (tt0) REVERT: F 234 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7787 (mt-10) outliers start: 89 outliers final: 75 residues processed: 634 average time/residue: 0.3398 time to fit residues: 337.3802 Evaluate side-chains 619 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 543 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 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 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 278 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 96 LYS 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 204 VAL Chi-restraints excluded: chain D residue 217 ARG 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 E residue 47 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 64 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 185 ILE Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 450 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 277 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 327 ASN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 429 HIS ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23448 Z= 0.277 Angle : 0.659 9.297 31680 Z= 0.333 Chirality : 0.046 0.187 3534 Planarity : 0.004 0.059 4062 Dihedral : 10.473 116.723 3456 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.74 % Allowed : 19.75 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2880 helix: 0.98 (0.16), residues: 1050 sheet: -0.09 (0.20), residues: 690 loop : -0.30 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 331 HIS 0.015 0.002 HIS C 429 PHE 0.026 0.002 PHE D 199 TYR 0.039 0.002 TYR A 402 ARG 0.009 0.000 ARG F 170 *********************** 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 657 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 566 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 235 TYR cc_start: 0.8506 (m-80) cc_final: 0.7917 (m-80) REVERT: B 234 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7669 (mt-10) REVERT: B 235 TYR cc_start: 0.8511 (m-80) cc_final: 0.8002 (m-80) REVERT: B 302 VAL cc_start: 0.9081 (m) cc_final: 0.8816 (t) REVERT: B 461 SER cc_start: 0.7825 (t) cc_final: 0.7581 (t) REVERT: C 194 TYR cc_start: 0.7469 (m-80) cc_final: 0.7155 (m-80) REVERT: C 234 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 469 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7087 (tt0) REVERT: D 194 TYR cc_start: 0.7567 (m-80) cc_final: 0.7192 (m-80) REVERT: D 235 TYR cc_start: 0.8572 (m-80) cc_final: 0.8181 (m-80) REVERT: D 247 PHE cc_start: 0.8470 (m-80) cc_final: 0.8229 (m-10) REVERT: D 385 ARG cc_start: 0.7729 (ttm170) cc_final: 0.7437 (ttm170) REVERT: E 187 GLU cc_start: 0.6445 (mp0) cc_final: 0.6181 (mp0) REVERT: E 234 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7565 (mt-10) REVERT: E 235 TYR cc_start: 0.8450 (m-80) cc_final: 0.7973 (m-80) REVERT: E 247 PHE cc_start: 0.8663 (m-80) cc_final: 0.8450 (m-80) REVERT: E 302 VAL cc_start: 0.8977 (m) cc_final: 0.8726 (t) REVERT: E 392 PHE cc_start: 0.8601 (t80) cc_final: 0.8307 (t80) REVERT: E 456 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8047 (t80) REVERT: F 86 ASN cc_start: 0.8234 (m-40) cc_final: 0.8004 (m-40) REVERT: F 185 ILE cc_start: 0.9205 (mt) cc_final: 0.8932 (mm) REVERT: F 194 TYR cc_start: 0.7410 (m-80) cc_final: 0.7175 (m-80) REVERT: F 234 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7752 (mt-10) outliers start: 91 outliers final: 76 residues processed: 614 average time/residue: 0.3495 time to fit residues: 338.7074 Evaluate side-chains 620 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 542 time to evaluate : 2.753 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 93 ASP 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 204 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 327 ASN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 185 ILE 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 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 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 ARG 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 365 SER Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 93 ASP 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 185 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 443 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 83 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 137 optimal weight: 0.1980 chunk 25 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 23448 Z= 0.279 Angle : 0.669 12.340 31680 Z= 0.337 Chirality : 0.046 0.225 3534 Planarity : 0.004 0.068 4062 Dihedral : 10.210 116.998 3456 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.29 % Allowed : 20.82 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2880 helix: 0.97 (0.16), residues: 1050 sheet: -0.15 (0.20), residues: 708 loop : -0.25 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 331 HIS 0.025 0.003 HIS D 429 PHE 0.035 0.002 PHE C 392 TYR 0.042 0.002 TYR A 402 ARG 0.010 0.001 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 566 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8501 (m-80) cc_final: 0.7911 (m-80) REVERT: A 469 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6711 (tm-30) REVERT: B 187 GLU cc_start: 0.6403 (mp0) cc_final: 0.6178 (mp0) REVERT: B 234 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 235 TYR cc_start: 0.8474 (m-80) cc_final: 0.7956 (m-80) REVERT: B 302 VAL cc_start: 0.9100 (m) cc_final: 0.8843 (t) REVERT: B 461 SER cc_start: 0.7787 (t) cc_final: 0.7587 (t) REVERT: C 187 GLU cc_start: 0.6493 (mp0) cc_final: 0.6150 (mp0) REVERT: C 194 TYR cc_start: 0.7419 (m-80) cc_final: 0.7175 (m-80) REVERT: C 234 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 362 ILE cc_start: 0.9067 (mm) cc_final: 0.8753 (mm) REVERT: C 469 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 194 TYR cc_start: 0.7448 (m-80) cc_final: 0.7137 (m-80) REVERT: D 235 TYR cc_start: 0.8580 (m-80) cc_final: 0.8114 (m-80) REVERT: D 247 PHE cc_start: 0.8542 (m-80) cc_final: 0.8067 (m-10) REVERT: D 361 GLN cc_start: 0.8319 (tp40) cc_final: 0.8064 (tp40) REVERT: E 187 GLU cc_start: 0.6395 (mp0) cc_final: 0.6140 (mp0) REVERT: E 234 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7560 (mt-10) REVERT: E 235 TYR cc_start: 0.8433 (m-80) cc_final: 0.7965 (m-80) REVERT: E 247 PHE cc_start: 0.8714 (m-80) cc_final: 0.8434 (m-80) REVERT: E 302 VAL cc_start: 0.9038 (m) cc_final: 0.8797 (t) REVERT: E 392 PHE cc_start: 0.8645 (t80) cc_final: 0.8359 (t80) REVERT: E 456 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7982 (t80) REVERT: F 86 ASN cc_start: 0.8304 (m-40) cc_final: 0.8084 (m-40) REVERT: F 185 ILE cc_start: 0.9216 (mt) cc_final: 0.8946 (mm) REVERT: F 194 TYR cc_start: 0.7444 (m-80) cc_final: 0.7199 (m-80) REVERT: F 234 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7722 (mt-10) outliers start: 80 outliers final: 74 residues processed: 608 average time/residue: 0.3264 time to fit residues: 313.3700 Evaluate side-chains 614 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 539 time to evaluate : 2.384 ------------------------------------------------------------------------------- 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 64 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 93 ASP 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 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 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 274 CYS 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 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 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 429 HIS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 93 ASP 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 185 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 456 PHE Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 443 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.0970 chunk 265 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 429 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23448 Z= 0.253 Angle : 0.663 11.571 31680 Z= 0.333 Chirality : 0.046 0.315 3534 Planarity : 0.004 0.043 4062 Dihedral : 9.917 117.646 3456 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.92 % Allowed : 21.98 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2880 helix: 1.01 (0.16), residues: 1050 sheet: -0.17 (0.20), residues: 708 loop : -0.28 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 331 HIS 0.018 0.002 HIS E 429 PHE 0.017 0.002 PHE B 59 TYR 0.043 0.002 TYR A 402 ARG 0.010 0.000 ARG B 216 *********************** 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 642 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 571 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8475 (m-80) cc_final: 0.7887 (m-80) REVERT: A 469 GLU cc_start: 0.6985 (tm-30) cc_final: 0.6740 (tm-30) REVERT: B 187 GLU cc_start: 0.6389 (mp0) cc_final: 0.6178 (mp0) REVERT: B 234 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 235 TYR cc_start: 0.8458 (m-80) cc_final: 0.7940 (m-80) REVERT: B 247 PHE cc_start: 0.8453 (m-80) cc_final: 0.8219 (m-10) REVERT: B 302 VAL cc_start: 0.9088 (m) cc_final: 0.8858 (t) REVERT: C 187 GLU cc_start: 0.6600 (mp0) cc_final: 0.6257 (mp0) REVERT: C 194 TYR cc_start: 0.7436 (m-80) cc_final: 0.7222 (m-80) REVERT: C 234 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 362 ILE cc_start: 0.9062 (mm) cc_final: 0.8793 (mm) REVERT: D 194 TYR cc_start: 0.7508 (m-80) cc_final: 0.7194 (m-80) REVERT: D 235 TYR cc_start: 0.8507 (m-80) cc_final: 0.8095 (m-80) REVERT: D 247 PHE cc_start: 0.8545 (m-80) cc_final: 0.8142 (m-80) REVERT: D 454 ASN cc_start: 0.7504 (t0) cc_final: 0.7195 (t0) REVERT: E 187 GLU cc_start: 0.6419 (mp0) cc_final: 0.6146 (mp0) REVERT: E 234 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7527 (mt-10) REVERT: E 235 TYR cc_start: 0.8418 (m-80) cc_final: 0.7892 (m-80) REVERT: E 247 PHE cc_start: 0.8685 (m-80) cc_final: 0.8439 (m-80) REVERT: E 302 VAL cc_start: 0.9031 (m) cc_final: 0.8827 (t) REVERT: E 392 PHE cc_start: 0.8622 (t80) cc_final: 0.8342 (t80) REVERT: F 86 ASN cc_start: 0.8270 (m-40) cc_final: 0.8039 (m-40) REVERT: F 185 ILE cc_start: 0.9210 (mt) cc_final: 0.8957 (mm) REVERT: F 187 GLU cc_start: 0.6258 (mp0) cc_final: 0.6055 (mp0) REVERT: F 194 TYR cc_start: 0.7373 (m-80) cc_final: 0.7171 (m-80) REVERT: F 234 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7717 (mt-10) outliers start: 71 outliers final: 61 residues processed: 605 average time/residue: 0.3484 time to fit residues: 336.8772 Evaluate side-chains 606 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 545 time to evaluate : 2.506 ------------------------------------------------------------------------------- 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 324 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 93 ASP 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 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 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER 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 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 167 LEU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 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 185 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 HIS ** F 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 GLN ** F 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23448 Z= 0.299 Angle : 0.686 9.035 31680 Z= 0.348 Chirality : 0.047 0.291 3534 Planarity : 0.004 0.054 4062 Dihedral : 9.851 117.971 3456 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.59 % Allowed : 22.76 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2880 helix: 0.97 (0.16), residues: 1050 sheet: -0.18 (0.20), residues: 708 loop : -0.37 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 331 HIS 0.017 0.003 HIS E 429 PHE 0.045 0.002 PHE B 392 TYR 0.039 0.002 TYR A 402 ARG 0.008 0.001 ARG B 385 ********************** 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 622 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 559 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8471 (m-80) cc_final: 0.7890 (m-80) REVERT: A 469 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 187 GLU cc_start: 0.6465 (mp0) cc_final: 0.6235 (mp0) REVERT: B 234 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 235 TYR cc_start: 0.8463 (m-80) cc_final: 0.7947 (m-80) REVERT: B 247 PHE cc_start: 0.8502 (m-80) cc_final: 0.8232 (m-10) REVERT: B 302 VAL cc_start: 0.9090 (m) cc_final: 0.8851 (t) REVERT: B 418 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7629 (mm-40) REVERT: C 187 GLU cc_start: 0.6466 (mp0) cc_final: 0.6128 (mp0) REVERT: C 194 TYR cc_start: 0.7385 (m-80) cc_final: 0.7170 (m-80) REVERT: C 234 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 362 ILE cc_start: 0.9068 (mm) cc_final: 0.8799 (mm) REVERT: C 469 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6560 (tt0) REVERT: E 187 GLU cc_start: 0.6431 (mp0) cc_final: 0.6168 (mp0) REVERT: E 234 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 235 TYR cc_start: 0.8446 (m-80) cc_final: 0.7897 (m-80) REVERT: E 392 PHE cc_start: 0.8619 (t80) cc_final: 0.8353 (t80) REVERT: F 185 ILE cc_start: 0.9200 (mt) cc_final: 0.8948 (mm) REVERT: F 194 TYR cc_start: 0.7402 (m-80) cc_final: 0.7190 (m-80) REVERT: F 234 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7776 (mt-10) outliers start: 63 outliers final: 61 residues processed: 590 average time/residue: 0.3313 time to fit residues: 310.6387 Evaluate side-chains 604 residues out of total 2454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 543 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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 324 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 93 ASP 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 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 93 ASP Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 158 SER 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 180 MET Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 57 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 185 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 272 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 443 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 81 GLN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 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 = 0.3748 r_free = 0.3748 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120629 restraints weight = 38254.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124408 restraints weight = 21521.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126930 restraints weight = 14620.959| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23448 Z= 0.216 Angle : 0.671 9.367 31680 Z= 0.337 Chirality : 0.046 0.270 3534 Planarity : 0.004 0.059 4062 Dihedral : 9.656 118.579 3456 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.26 % Allowed : 23.29 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2880 helix: 1.00 (0.16), residues: 1050 sheet: -0.22 (0.19), residues: 768 loop : -0.41 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 331 HIS 0.021 0.002 HIS E 429 PHE 0.042 0.002 PHE F 392 TYR 0.044 0.001 TYR A 402 ARG 0.010 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5997.90 seconds wall clock time: 106 minutes 55.95 seconds (6415.95 seconds total)