Starting phenix.real_space_refine on Thu Sep 26 13:43:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfd_31949/09_2024/7vfd_31949.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfd_31949/09_2024/7vfd_31949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfd_31949/09_2024/7vfd_31949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfd_31949/09_2024/7vfd_31949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfd_31949/09_2024/7vfd_31949.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vfd_31949/09_2024/7vfd_31949.cif" } resolution = 2.25 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8250 2.51 5 N 2100 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13262 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 541, 4290 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 bond proxies already assigned to first conformer: 4372 Chain: "B" Number of atoms: 4304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 541, 4290 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 bond proxies already assigned to first conformer: 4372 Chain: "C" Number of atoms: 4304 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 541, 4290 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 bond proxies already assigned to first conformer: 4372 Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ACYS A 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 94 " occ=0.50 residue: pdb=" N ACYS B 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 94 " occ=0.50 residue: pdb=" N ACYS C 94 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 94 " occ=0.50 Time building chain proxies: 13.48, per 1000 atoms: 1.02 Number of scatterers: 13262 At special positions: 0 Unit cell: (98.42, 99.456, 107.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2870 8.00 N 2100 7.00 C 8250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 3.0 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 36 sheets defined 21.3% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.901A pdb=" N LEU A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.682A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.536A pdb=" N SER A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.027A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.557A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.869A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.901A pdb=" N LEU B 9 " --> pdb=" O ILE B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.682A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.536A pdb=" N SER B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 4.027A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.557A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.868A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 2 through 9 removed outlier: 3.902A pdb=" N LEU C 9 " --> pdb=" O ILE C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.682A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.535A pdb=" N SER C 169 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.026A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.557A pdb=" N THR C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.869A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 401' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.880A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.880A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.180A pdb=" N SER A 102 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236 removed outlier: 3.812A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.578A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.041A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 299 Processing sheet with id=AB2, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.725A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.880A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.880A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 44 removed outlier: 6.179A pdb=" N SER B 102 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AB8, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB9, first strand: chain 'B' and resid 227 through 236 removed outlier: 3.811A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.579A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.042A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 Processing sheet with id=AC4, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AC5, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.726A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AC7, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.880A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.880A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.179A pdb=" N SER C 102 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AD2, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AD3, first strand: chain 'C' and resid 227 through 236 removed outlier: 3.812A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.577A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.041A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 269 through 270 Processing sheet with id=AD7, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AD8, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.725A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE C 365 " --> pdb=" O HIS C 386 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS C 386 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 367 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE C 384 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR C 369 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 349 through 350 543 hydrogen bonds defined for protein. 1413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4134 1.34 - 1.46: 2553 1.46 - 1.57: 6432 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 13188 Sorted by residual: bond pdb=" C HIS C 383 " pdb=" N ILE C 384 " ideal model delta sigma weight residual 1.331 1.296 0.034 1.27e-02 6.20e+03 7.30e+00 bond pdb=" C HIS B 383 " pdb=" N ILE B 384 " ideal model delta sigma weight residual 1.331 1.296 0.034 1.27e-02 6.20e+03 7.27e+00 bond pdb=" C HIS A 383 " pdb=" N ILE A 384 " ideal model delta sigma weight residual 1.331 1.296 0.034 1.27e-02 6.20e+03 7.19e+00 bond pdb=" CA ALA C 251 " pdb=" C ALA C 251 " ideal model delta sigma weight residual 1.533 1.520 0.013 9.60e-03 1.09e+04 1.80e+00 bond pdb=" CA ALA A 251 " pdb=" C ALA A 251 " ideal model delta sigma weight residual 1.533 1.520 0.013 9.60e-03 1.09e+04 1.80e+00 ... (remaining 13183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 17589 1.45 - 2.90: 293 2.90 - 4.35: 37 4.35 - 5.80: 12 5.80 - 7.25: 9 Bond angle restraints: 17940 Sorted by residual: angle pdb=" O PHE C 381 " pdb=" C PHE C 381 " pdb=" N ALA C 382 " ideal model delta sigma weight residual 123.06 127.47 -4.41 1.12e+00 7.97e-01 1.55e+01 angle pdb=" O PHE A 381 " pdb=" C PHE A 381 " pdb=" N ALA A 382 " ideal model delta sigma weight residual 123.06 127.45 -4.39 1.12e+00 7.97e-01 1.53e+01 angle pdb=" O PHE B 381 " pdb=" C PHE B 381 " pdb=" N ALA B 382 " ideal model delta sigma weight residual 123.06 127.42 -4.36 1.12e+00 7.97e-01 1.52e+01 angle pdb=" CA PHE C 381 " pdb=" C PHE C 381 " pdb=" N ALA C 382 " ideal model delta sigma weight residual 115.51 110.74 4.77 1.24e+00 6.50e-01 1.48e+01 angle pdb=" CA PHE A 381 " pdb=" C PHE A 381 " pdb=" N ALA A 382 " ideal model delta sigma weight residual 115.51 110.80 4.71 1.24e+00 6.50e-01 1.44e+01 ... (remaining 17935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7469 17.78 - 35.56: 355 35.56 - 53.34: 69 53.34 - 71.12: 24 71.12 - 88.90: 18 Dihedral angle restraints: 7935 sinusoidal: 3117 harmonic: 4818 Sorted by residual: dihedral pdb=" CA THR B 491 " pdb=" C THR B 491 " pdb=" N ILE B 492 " pdb=" CA ILE B 492 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR C 491 " pdb=" C THR C 491 " pdb=" N ILE C 492 " pdb=" CA ILE C 492 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR A 491 " pdb=" C THR A 491 " pdb=" N ILE A 492 " pdb=" CA ILE A 492 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1095 0.028 - 0.055: 544 0.055 - 0.083: 191 0.083 - 0.111: 195 0.111 - 0.139: 54 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CA ILE B 100 " pdb=" N ILE B 100 " pdb=" C ILE B 100 " pdb=" CB ILE B 100 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 100 " pdb=" N ILE A 100 " pdb=" C ILE A 100 " pdb=" CB ILE A 100 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE C 100 " pdb=" N ILE C 100 " pdb=" C ILE C 100 " pdb=" CB ILE C 100 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2076 not shown) Planarity restraints: 2289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 381 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C PHE B 381 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE B 381 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA B 382 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 381 " 0.006 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C PHE A 381 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE A 381 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A 382 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 381 " 0.006 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C PHE C 381 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE C 381 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA C 382 " 0.008 2.00e-02 2.50e+03 ... (remaining 2286 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1113 2.74 - 3.28: 13238 3.28 - 3.82: 23658 3.82 - 4.36: 29289 4.36 - 4.90: 47645 Nonbonded interactions: 114943 Sorted by model distance: nonbonded pdb=" OE1 GLU C 74 " pdb=" OG1 THR C 153 " model vdw 2.204 3.040 nonbonded pdb=" OE1 GLU B 74 " pdb=" OG1 THR B 153 " model vdw 2.205 3.040 nonbonded pdb=" OE1 GLU A 74 " pdb=" OG1 THR A 153 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP B 410 " pdb=" O HOH B 601 " model vdw 2.234 3.040 nonbonded pdb=" O VAL B 219 " pdb=" O HOH B 602 " model vdw 2.245 3.040 ... (remaining 114938 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 0 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'B' and (resid 0 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'C' and (resid 0 through 93 or resid 95 through 356 or resid 358 through \ 547)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 40.250 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.004 0.034 13188 Z= 0.238 Angle : 0.531 7.251 17940 Z= 0.304 Chirality : 0.047 0.139 2079 Planarity : 0.004 0.033 2289 Dihedral : 12.473 88.901 4833 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.60 % Allowed : 3.87 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1614 helix: -1.56 (0.25), residues: 261 sheet: 0.47 (0.24), residues: 459 loop : -0.49 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 108 HIS 0.004 0.001 HIS C 383 PHE 0.015 0.002 PHE C 199 TYR 0.011 0.002 TYR B 519 ARG 0.005 0.001 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 236 time to evaluate : 1.601 Fit side-chains REVERT: A 1 MET cc_start: 0.7163 (mmt) cc_final: 0.6840 (mmt) REVERT: A 204 LYS cc_start: 0.8268 (ttpp) cc_final: 0.8065 (mtpp) REVERT: B 309 SER cc_start: 0.8716 (m) cc_final: 0.8437 (p) REVERT: B 486 PHE cc_start: 0.8861 (m-80) cc_final: 0.8622 (m-80) REVERT: C 33 MET cc_start: 0.8751 (tpt) cc_final: 0.8350 (tpp) REVERT: C 279 ASP cc_start: 0.7688 (m-30) cc_final: 0.7428 (m-30) outliers start: 9 outliers final: 4 residues processed: 242 average time/residue: 1.4102 time to fit residues: 368.8443 Evaluate side-chains 190 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain C residue 90 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 104 ASN A 203 ASN A 223 GLN A 324 GLN B 61 GLN B 104 ASN C 104 ASN C 117 ASN C 403 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13188 Z= 0.260 Angle : 0.552 6.541 17940 Z= 0.303 Chirality : 0.050 0.161 2079 Planarity : 0.004 0.045 2289 Dihedral : 4.992 36.564 1776 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.34 % Allowed : 9.49 % Favored : 89.18 % 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: -0.09 (0.20), residues: 1614 helix: -0.51 (0.30), residues: 258 sheet: 0.50 (0.22), residues: 483 loop : -0.13 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 108 HIS 0.005 0.001 HIS C 128 PHE 0.017 0.002 PHE C 199 TYR 0.014 0.002 TYR A 520 ARG 0.004 0.001 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.487 Fit side-chains REVERT: A 111 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: A 204 LYS cc_start: 0.8220 (ttpp) cc_final: 0.8005 (mtpp) REVERT: B 74 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7498 (mm-30) REVERT: B 111 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7693 (mm-30) REVERT: B 486 PHE cc_start: 0.8827 (m-80) cc_final: 0.8574 (m-80) REVERT: C 33 MET cc_start: 0.8679 (tpt) cc_final: 0.8307 (tpp) outliers start: 20 outliers final: 8 residues processed: 203 average time/residue: 1.3574 time to fit residues: 298.7265 Evaluate side-chains 185 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 100 optimal weight: 0.0370 chunk 40 optimal weight: 6.9990 chunk 147 optimal weight: 0.2980 chunk 159 optimal weight: 0.4980 chunk 131 optimal weight: 0.0770 chunk 146 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 35 GLN B 324 GLN C 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13188 Z= 0.114 Angle : 0.442 5.245 17940 Z= 0.238 Chirality : 0.046 0.152 2079 Planarity : 0.003 0.036 2289 Dihedral : 4.240 32.337 1775 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.53 % Allowed : 10.75 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1614 helix: -0.10 (0.32), residues: 264 sheet: 0.64 (0.23), residues: 483 loop : 0.11 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 108 HIS 0.002 0.000 HIS C 128 PHE 0.009 0.001 PHE A 199 TYR 0.009 0.001 TYR C 283 ARG 0.002 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 1.554 Fit side-chains REVERT: B 74 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: B 486 PHE cc_start: 0.8779 (m-80) cc_final: 0.8574 (m-80) REVERT: B 539 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6343 (pt0) REVERT: C 33 MET cc_start: 0.8520 (tpt) cc_final: 0.8119 (tpp) REVERT: C 61 GLN cc_start: 0.8097 (pt0) cc_final: 0.7709 (pt0) outliers start: 8 outliers final: 3 residues processed: 192 average time/residue: 1.3239 time to fit residues: 277.1477 Evaluate side-chains 174 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 539 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 0.2980 chunk 156 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN B 203 ASN C 203 ASN C 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13188 Z= 0.172 Angle : 0.481 5.232 17940 Z= 0.262 Chirality : 0.048 0.149 2079 Planarity : 0.003 0.034 2289 Dihedral : 4.450 33.080 1773 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.94 % Allowed : 10.89 % Favored : 88.18 % 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: 0.32 (0.20), residues: 1614 helix: 0.10 (0.32), residues: 261 sheet: 0.64 (0.23), residues: 483 loop : 0.13 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 108 HIS 0.003 0.001 HIS C 128 PHE 0.015 0.001 PHE C 199 TYR 0.012 0.001 TYR B 520 ARG 0.002 0.000 ARG C 475 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.599 Fit side-chains REVERT: A 111 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7560 (mm-30) REVERT: B 111 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: B 539 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.6406 (pt0) REVERT: C 33 MET cc_start: 0.8648 (tpt) cc_final: 0.8272 (tpp) REVERT: C 61 GLN cc_start: 0.8091 (pt0) cc_final: 0.7704 (pt0) outliers start: 14 outliers final: 5 residues processed: 176 average time/residue: 1.5088 time to fit residues: 287.7753 Evaluate side-chains 173 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 539 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9980 chunk 88 optimal weight: 0.0020 chunk 2 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13188 Z= 0.186 Angle : 0.489 5.357 17940 Z= 0.267 Chirality : 0.048 0.147 2079 Planarity : 0.003 0.033 2289 Dihedral : 4.535 32.990 1773 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.00 % Allowed : 11.29 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1614 helix: 0.11 (0.32), residues: 261 sheet: 0.65 (0.22), residues: 480 loop : 0.10 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 108 HIS 0.003 0.001 HIS C 128 PHE 0.016 0.002 PHE A 199 TYR 0.013 0.002 TYR B 520 ARG 0.004 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.419 Fit side-chains REVERT: A 35 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: A 111 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: A 200 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: B 35 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7929 (tp40) REVERT: B 111 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: B 539 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: C 33 MET cc_start: 0.8654 (tpt) cc_final: 0.8338 (tpp) REVERT: C 61 GLN cc_start: 0.8085 (pt0) cc_final: 0.7709 (pt0) outliers start: 15 outliers final: 6 residues processed: 174 average time/residue: 1.4611 time to fit residues: 274.6589 Evaluate side-chains 177 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 539 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13188 Z= 0.141 Angle : 0.460 5.393 17940 Z= 0.249 Chirality : 0.047 0.148 2079 Planarity : 0.003 0.038 2289 Dihedral : 4.316 31.502 1773 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.87 % Allowed : 11.62 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.44 (0.20), residues: 1614 helix: 0.24 (0.33), residues: 261 sheet: 0.73 (0.23), residues: 450 loop : 0.20 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.003 0.001 HIS C 128 PHE 0.012 0.001 PHE A 199 TYR 0.009 0.001 TYR A 520 ARG 0.009 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 2.129 Fit side-chains REVERT: A 111 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: A 200 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: B 35 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7938 (tp40) REVERT: B 61 GLN cc_start: 0.7932 (pt0) cc_final: 0.7512 (pt0) REVERT: B 111 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: C 33 MET cc_start: 0.8590 (tpt) cc_final: 0.8145 (tpp) REVERT: C 61 GLN cc_start: 0.8079 (pt0) cc_final: 0.7708 (pt0) outliers start: 13 outliers final: 4 residues processed: 180 average time/residue: 1.5430 time to fit residues: 301.6429 Evaluate side-chains 177 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 482 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 114 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 203 ASN C 203 ASN C 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13188 Z= 0.317 Angle : 0.572 6.275 17940 Z= 0.315 Chirality : 0.051 0.150 2079 Planarity : 0.004 0.042 2289 Dihedral : 4.901 35.085 1773 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.14 % Allowed : 11.36 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.20), residues: 1614 helix: 0.01 (0.32), residues: 261 sheet: 0.47 (0.22), residues: 486 loop : 0.07 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 108 HIS 0.005 0.002 HIS B 386 PHE 0.018 0.002 PHE C 199 TYR 0.019 0.002 TYR B 520 ARG 0.010 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.515 Fit side-chains REVERT: A 111 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: A 200 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: A 204 LYS cc_start: 0.8271 (ttpp) cc_final: 0.8052 (mtpp) REVERT: B 35 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7858 (tp40) REVERT: B 61 GLN cc_start: 0.7973 (pt0) cc_final: 0.7555 (pt0) REVERT: B 111 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: C 33 MET cc_start: 0.8735 (tpt) cc_final: 0.8415 (tpp) REVERT: C 61 GLN cc_start: 0.8114 (pt0) cc_final: 0.7752 (pt0) outliers start: 17 outliers final: 9 residues processed: 182 average time/residue: 1.4240 time to fit residues: 280.0594 Evaluate side-chains 184 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.0010 chunk 14 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13188 Z= 0.122 Angle : 0.451 5.852 17940 Z= 0.243 Chirality : 0.047 0.152 2079 Planarity : 0.003 0.040 2289 Dihedral : 4.245 30.940 1773 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.60 % Allowed : 11.96 % Favored : 87.44 % 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: 0.45 (0.20), residues: 1614 helix: 0.20 (0.33), residues: 264 sheet: 0.73 (0.24), residues: 441 loop : 0.23 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.002 0.001 HIS A 128 PHE 0.015 0.001 BPHE B 357 TYR 0.008 0.001 TYR A 520 ARG 0.009 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 1.631 Fit side-chains REVERT: A 111 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: A 134 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 203 ASN cc_start: 0.8528 (t0) cc_final: 0.8261 (t0) REVERT: B 35 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7926 (tp40) REVERT: B 61 GLN cc_start: 0.7906 (pt0) cc_final: 0.7491 (pt0) REVERT: B 111 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: C 33 MET cc_start: 0.8569 (tpt) cc_final: 0.8149 (tpp) REVERT: C 61 GLN cc_start: 0.8078 (pt0) cc_final: 0.7724 (pt0) outliers start: 9 outliers final: 3 residues processed: 176 average time/residue: 1.3946 time to fit residues: 266.0140 Evaluate side-chains 177 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 482 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.0770 chunk 137 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN C 203 ASN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13188 Z= 0.305 Angle : 0.565 6.641 17940 Z= 0.310 Chirality : 0.051 0.147 2079 Planarity : 0.004 0.041 2289 Dihedral : 4.853 34.863 1773 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.80 % Allowed : 11.82 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.20), residues: 1614 helix: 0.10 (0.32), residues: 261 sheet: 0.48 (0.23), residues: 486 loop : 0.10 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 108 HIS 0.005 0.002 HIS B 386 PHE 0.017 0.002 PHE C 199 TYR 0.019 0.002 TYR B 520 ARG 0.011 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.530 Fit side-chains REVERT: A 111 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: A 200 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7022 (tt0) REVERT: A 204 LYS cc_start: 0.8254 (ttpp) cc_final: 0.8033 (mtpp) REVERT: B 35 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7890 (tp40) REVERT: B 61 GLN cc_start: 0.7947 (pt0) cc_final: 0.7554 (pt0) REVERT: B 111 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7678 (mm-30) REVERT: C 33 MET cc_start: 0.8722 (tpt) cc_final: 0.8291 (tpp) REVERT: C 61 GLN cc_start: 0.8069 (pt0) cc_final: 0.7722 (pt0) outliers start: 12 outliers final: 7 residues processed: 181 average time/residue: 1.4415 time to fit residues: 282.4701 Evaluate side-chains 183 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 161 optimal weight: 0.0170 chunk 148 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13188 Z= 0.141 Angle : 0.467 6.098 17940 Z= 0.253 Chirality : 0.047 0.149 2079 Planarity : 0.003 0.041 2289 Dihedral : 4.389 31.899 1773 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.60 % Allowed : 11.96 % Favored : 87.44 % 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: 0.44 (0.20), residues: 1614 helix: 0.22 (0.33), residues: 261 sheet: 0.72 (0.24), residues: 441 loop : 0.21 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 108 HIS 0.003 0.001 HIS C 128 PHE 0.013 0.001 PHE A 199 TYR 0.010 0.001 TYR A 520 ARG 0.011 0.000 ARG B 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 1.637 Fit side-chains REVERT: A 111 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: A 134 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: B 35 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: B 61 GLN cc_start: 0.7887 (pt0) cc_final: 0.7474 (pt0) REVERT: B 111 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: C 33 MET cc_start: 0.8583 (tpt) cc_final: 0.8234 (tpp) REVERT: C 61 GLN cc_start: 0.8090 (pt0) cc_final: 0.7744 (pt0) outliers start: 9 outliers final: 4 residues processed: 175 average time/residue: 1.5845 time to fit residues: 299.6995 Evaluate side-chains 180 residues out of total 1491 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 482 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 35 optimal weight: 0.0870 chunk 128 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 chunk 113 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN C 203 ASN C 334 ASN C 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.097322 restraints weight = 17587.219| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.71 r_work: 0.2875 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13188 Z= 0.146 Angle : 0.465 6.267 17940 Z= 0.252 Chirality : 0.047 0.147 2079 Planarity : 0.003 0.042 2289 Dihedral : 4.313 31.312 1773 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.80 % Allowed : 11.96 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.21), residues: 1614 helix: -0.10 (0.32), residues: 282 sheet: 0.80 (0.24), residues: 438 loop : 0.25 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.002 0.001 HIS C 128 PHE 0.013 0.001 BPHE B 357 TYR 0.010 0.001 TYR C 258 ARG 0.008 0.000 ARG B 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5343.67 seconds wall clock time: 94 minutes 13.27 seconds (5653.27 seconds total)