Starting phenix.real_space_refine on Thu Jul 31 07:40:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vfd_31949/07_2025/7vfd_31949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfd_31949/07_2025/7vfd_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/cci-nas-00/data/ceres_data/7vfd_31949/07_2025/7vfd_31949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfd_31949/07_2025/7vfd_31949.map" model { file = "/net/cci-nas-00/data/ceres_data/7vfd_31949/07_2025/7vfd_31949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfd_31949/07_2025/7vfd_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 13.33, per 1000 atoms: 1.01 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: 3.18 Conformation dependent library (CDL) restraints added in 2.8 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: 2.10 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: 5.09 Time building geometry restraints manager: 3.79 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.100 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.250 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:16.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.590 ------------------------------------------------------------------------------- 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= 0.167 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 Details of bonding type rmsd hydrogen bonds : bond 0.15596 ( 483) hydrogen bonds : angle 6.98135 ( 1413) covalent geometry : bond 0.00357 (13188) covalent geometry : angle 0.53089 (17940) *********************** 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 to be fit. rotamer outliers: 9 poor density : 236 time to evaluate : 1.481 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: 1.3705 time to fit residues: 358.8049 Evaluate side-chains 190 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092513 restraints weight = 23502.451| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.01 r_work: 0.2793 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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= 0.175 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 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 483) hydrogen bonds : angle 5.52495 ( 1413) covalent geometry : bond 0.00393 (13188) covalent geometry : angle 0.55153 (17940) *********************** 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 to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 1.578 Fit side-chains REVERT: A 1 MET cc_start: 0.7870 (mmt) cc_final: 0.7381 (mmt) REVERT: A 62 TYR cc_start: 0.8329 (m-80) cc_final: 0.8102 (m-80) REVERT: A 111 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8542 (mm-30) REVERT: A 204 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8364 (mtpp) REVERT: B 74 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8436 (mm-30) REVERT: B 111 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8469 (mm-30) REVERT: B 309 SER cc_start: 0.8811 (m) cc_final: 0.8489 (p) REVERT: B 486 PHE cc_start: 0.8654 (m-80) cc_final: 0.8379 (m-80) REVERT: C 33 MET cc_start: 0.9262 (tpt) cc_final: 0.8991 (tpp) REVERT: C 378 ARG cc_start: 0.8184 (ptm-80) cc_final: 0.7944 (ptm-80) outliers start: 20 outliers final: 8 residues processed: 203 average time/residue: 1.3602 time to fit residues: 299.7541 Evaluate side-chains 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 2 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 118 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094684 restraints weight = 26529.081| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.20 r_work: 0.2898 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1710 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= 0.098 Angle : 0.459 5.451 17940 Z= 0.249 Chirality : 0.047 0.154 2079 Planarity : 0.003 0.037 2289 Dihedral : 4.410 33.389 1775 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.60 % Allowed : 10.69 % 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: 0.23 (0.20), residues: 1614 helix: -0.06 (0.32), residues: 261 sheet: 0.62 (0.23), residues: 483 loop : 0.06 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 108 HIS 0.003 0.001 HIS C 128 PHE 0.012 0.001 PHE A 199 TYR 0.008 0.001 TYR A 520 ARG 0.002 0.000 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 483) hydrogen bonds : angle 5.01203 ( 1413) covalent geometry : bond 0.00206 (13188) covalent geometry : angle 0.45901 (17940) *********************** 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 to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 1.397 Fit side-chains REVERT: A 1 MET cc_start: 0.7900 (mmt) cc_final: 0.7188 (mmt) REVERT: A 62 TYR cc_start: 0.8195 (m-80) cc_final: 0.7978 (m-10) REVERT: A 111 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8515 (mm-30) REVERT: B 74 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8437 (mm-30) REVERT: B 146 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: B 309 SER cc_start: 0.8869 (m) cc_final: 0.8633 (p) REVERT: B 486 PHE cc_start: 0.8698 (m-80) cc_final: 0.8461 (m-80) REVERT: B 539 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: C 33 MET cc_start: 0.9229 (tpt) cc_final: 0.8961 (tpp) REVERT: C 61 GLN cc_start: 0.8493 (pt0) cc_final: 0.8146 (pt0) REVERT: C 378 ARG cc_start: 0.8241 (ptm-80) cc_final: 0.7994 (ptm-80) outliers start: 9 outliers final: 2 residues processed: 191 average time/residue: 1.3270 time to fit residues: 276.1264 Evaluate side-chains 178 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 146 ASP 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 40 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.089755 restraints weight = 28291.427| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.29 r_work: 0.2796 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1675 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= 0.216 Angle : 0.582 5.707 17940 Z= 0.321 Chirality : 0.051 0.152 2079 Planarity : 0.004 0.044 2289 Dihedral : 4.996 36.660 1773 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.60 % Allowed : 10.29 % Favored : 88.11 % 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: 0.06 (0.20), residues: 1614 helix: -0.11 (0.31), residues: 258 sheet: 0.47 (0.22), residues: 483 loop : -0.06 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 108 HIS 0.005 0.002 HIS B 386 PHE 0.019 0.002 PHE C 199 TYR 0.018 0.002 TYR B 520 ARG 0.004 0.001 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 483) hydrogen bonds : angle 5.41604 ( 1413) covalent geometry : bond 0.00497 (13188) covalent geometry : angle 0.58191 (17940) *********************** 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 196 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.392 Fit side-chains REVERT: A 1 MET cc_start: 0.7825 (mmt) cc_final: 0.7110 (mmt) REVERT: A 62 TYR cc_start: 0.8286 (m-80) cc_final: 0.8082 (m-80) REVERT: A 111 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8576 (mm-30) REVERT: A 204 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8373 (mtpp) REVERT: B 24 VAL cc_start: 0.8085 (p) cc_final: 0.7869 (m) REVERT: B 111 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8560 (mm-30) REVERT: B 309 SER cc_start: 0.8835 (m) cc_final: 0.8563 (p) REVERT: B 353 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7633 (mtp-110) REVERT: B 498 ARG cc_start: 0.6930 (tpp80) cc_final: 0.6687 (ttm-80) REVERT: B 539 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: C 33 MET cc_start: 0.9308 (tpt) cc_final: 0.9091 (tpp) REVERT: C 61 GLN cc_start: 0.8474 (pt0) cc_final: 0.8151 (pt0) outliers start: 24 outliers final: 11 residues processed: 186 average time/residue: 1.5935 time to fit residues: 320.7773 Evaluate side-chains 188 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 220 LYS 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 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 539 GLN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 404 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 0.0010 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.091557 restraints weight = 28139.160| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.18 r_work: 0.2775 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1725 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= 0.169 Angle : 0.533 5.999 17940 Z= 0.292 Chirality : 0.049 0.151 2079 Planarity : 0.004 0.037 2289 Dihedral : 4.847 35.682 1773 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.14 % Allowed : 10.62 % Favored : 88.24 % 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: 0.11 (0.20), residues: 1614 helix: -0.05 (0.31), residues: 261 sheet: 0.51 (0.22), residues: 483 loop : -0.03 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 108 HIS 0.004 0.001 HIS C 128 PHE 0.016 0.002 PHE C 199 TYR 0.014 0.002 TYR B 520 ARG 0.004 0.001 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 483) hydrogen bonds : angle 5.26008 ( 1413) covalent geometry : bond 0.00382 (13188) covalent geometry : angle 0.53267 (17940) *********************** 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 191 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.643 Fit side-chains REVERT: A 1 MET cc_start: 0.7764 (mmt) cc_final: 0.7125 (mmt) REVERT: A 111 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8538 (mm-30) REVERT: B 35 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8681 (tp40) REVERT: B 111 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8493 (mm-30) REVERT: B 146 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: B 309 SER cc_start: 0.8809 (m) cc_final: 0.8563 (p) REVERT: B 498 ARG cc_start: 0.6905 (tpp80) cc_final: 0.6640 (ttm-80) REVERT: C 4 THR cc_start: 0.5811 (OUTLIER) cc_final: 0.5441 (t) REVERT: C 33 MET cc_start: 0.9260 (tpt) cc_final: 0.9022 (tpp) REVERT: C 61 GLN cc_start: 0.8491 (pt0) cc_final: 0.8172 (pt0) REVERT: C 354 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7490 (mptp) outliers start: 17 outliers final: 7 residues processed: 183 average time/residue: 1.9320 time to fit residues: 382.6650 Evaluate side-chains 183 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 35 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 123 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 ASN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.090433 restraints weight = 29190.622| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.23 r_work: 0.2777 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13188 Z= 0.171 Angle : 0.538 5.880 17940 Z= 0.295 Chirality : 0.049 0.150 2079 Planarity : 0.004 0.038 2289 Dihedral : 4.865 36.069 1773 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.27 % Allowed : 10.96 % Favored : 87.78 % 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: 0.13 (0.20), residues: 1614 helix: 0.01 (0.32), residues: 261 sheet: 0.51 (0.23), residues: 483 loop : -0.02 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 108 HIS 0.004 0.001 HIS C 128 PHE 0.017 0.002 PHE C 199 TYR 0.015 0.002 TYR B 520 ARG 0.003 0.001 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 483) hydrogen bonds : angle 5.28577 ( 1413) covalent geometry : bond 0.00386 (13188) covalent geometry : angle 0.53847 (17940) *********************** 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 193 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.660 Fit side-chains REVERT: A 1 MET cc_start: 0.7803 (mmt) cc_final: 0.7359 (mmt) REVERT: A 111 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8580 (mm-30) REVERT: B 35 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8665 (tp40) REVERT: B 111 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8493 (mm-30) REVERT: B 146 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: B 309 SER cc_start: 0.8796 (m) cc_final: 0.8537 (p) REVERT: B 498 ARG cc_start: 0.6871 (tpp80) cc_final: 0.6611 (ttm-80) REVERT: C 4 THR cc_start: 0.5797 (OUTLIER) cc_final: 0.5458 (t) REVERT: C 33 MET cc_start: 0.9283 (tpt) cc_final: 0.9041 (tpp) REVERT: C 61 GLN cc_start: 0.8490 (pt0) cc_final: 0.8180 (pt0) REVERT: C 354 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7470 (mptp) outliers start: 19 outliers final: 8 residues processed: 186 average time/residue: 1.4296 time to fit residues: 288.5728 Evaluate side-chains 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 35 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 404 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 61 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 159 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 334 ASN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.119331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.094204 restraints weight = 24384.506| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.03 r_work: 0.2814 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1823 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= 0.125 Angle : 0.489 5.879 17940 Z= 0.266 Chirality : 0.048 0.149 2079 Planarity : 0.003 0.036 2289 Dihedral : 4.593 34.147 1773 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.00 % Allowed : 11.36 % Favored : 87.64 % 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: 0.30 (0.20), residues: 1614 helix: 0.14 (0.32), residues: 261 sheet: 0.71 (0.24), residues: 438 loop : 0.07 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 108 HIS 0.003 0.001 HIS C 128 PHE 0.016 0.002 PHE A 199 TYR 0.012 0.001 TYR B 520 ARG 0.003 0.000 ARG C 475 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 483) hydrogen bonds : angle 5.08604 ( 1413) covalent geometry : bond 0.00273 (13188) covalent geometry : angle 0.48879 (17940) *********************** 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 192 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 1.631 Fit side-chains REVERT: A 1 MET cc_start: 0.7739 (mmt) cc_final: 0.7311 (mmt) REVERT: A 111 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8469 (mm-30) REVERT: B 35 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8666 (tp40) REVERT: B 61 GLN cc_start: 0.8311 (pt0) cc_final: 0.7886 (pt0) REVERT: B 111 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (mm-30) REVERT: B 309 SER cc_start: 0.8798 (m) cc_final: 0.8579 (p) REVERT: B 498 ARG cc_start: 0.6934 (tpp80) cc_final: 0.6683 (ttm-80) REVERT: C 4 THR cc_start: 0.5787 (OUTLIER) cc_final: 0.5463 (t) REVERT: C 33 MET cc_start: 0.9225 (tpt) cc_final: 0.8974 (tpp) REVERT: C 61 GLN cc_start: 0.8513 (pt0) cc_final: 0.8192 (pt0) REVERT: C 378 ARG cc_start: 0.8204 (ptm-80) cc_final: 0.7918 (ptm-80) outliers start: 15 outliers final: 7 residues processed: 186 average time/residue: 1.4357 time to fit residues: 289.6155 Evaluate side-chains 181 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 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 482 THR Chi-restraints excluded: chain C residue 4 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 134 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 ASN C 334 ASN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.091852 restraints weight = 28670.054| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.21 r_work: 0.2782 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13188 Z= 0.154 Angle : 0.521 5.916 17940 Z= 0.285 Chirality : 0.049 0.148 2079 Planarity : 0.004 0.037 2289 Dihedral : 4.740 34.966 1773 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.00 % Allowed : 11.69 % Favored : 87.31 % 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: 0.21 (0.20), residues: 1614 helix: 0.13 (0.32), residues: 261 sheet: 0.53 (0.23), residues: 483 loop : 0.04 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 108 HIS 0.003 0.001 HIS C 128 PHE 0.017 0.002 PHE A 199 TYR 0.014 0.002 TYR C 520 ARG 0.003 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 483) hydrogen bonds : angle 5.21452 ( 1413) covalent geometry : bond 0.00345 (13188) covalent geometry : angle 0.52126 (17940) *********************** 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 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.461 Fit side-chains REVERT: A 1 MET cc_start: 0.7778 (mmt) cc_final: 0.7338 (mmt) REVERT: A 111 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: B 35 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8678 (tp40) REVERT: B 59 ARG cc_start: 0.8215 (tmt170) cc_final: 0.7788 (tpt-90) REVERT: B 61 GLN cc_start: 0.8333 (pt0) cc_final: 0.7934 (pt0) REVERT: B 111 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8506 (mm-30) REVERT: B 309 SER cc_start: 0.8802 (m) cc_final: 0.8580 (p) REVERT: B 498 ARG cc_start: 0.6963 (tpp80) cc_final: 0.6711 (ttm-80) REVERT: C 4 THR cc_start: 0.5723 (OUTLIER) cc_final: 0.5443 (t) REVERT: C 33 MET cc_start: 0.9263 (tpt) cc_final: 0.8955 (tpp) REVERT: C 61 GLN cc_start: 0.8530 (pt0) cc_final: 0.8224 (pt0) REVERT: C 354 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7538 (mptp) outliers start: 15 outliers final: 8 residues processed: 178 average time/residue: 1.5025 time to fit residues: 288.9758 Evaluate side-chains 183 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 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 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 23 optimal weight: 0.0040 chunk 108 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN C 334 ASN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.094356 restraints weight = 23529.081| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.99 r_work: 0.2819 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1843 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= 0.128 Angle : 0.493 6.355 17940 Z= 0.268 Chirality : 0.048 0.148 2079 Planarity : 0.003 0.037 2289 Dihedral : 4.601 34.009 1773 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.00 % Allowed : 11.62 % 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: 0.32 (0.20), residues: 1614 helix: 0.17 (0.32), residues: 261 sheet: 0.70 (0.24), residues: 438 loop : 0.09 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 108 HIS 0.002 0.001 HIS B 250 PHE 0.016 0.002 PHE A 199 TYR 0.012 0.001 TYR B 520 ARG 0.003 0.000 ARG C 475 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 483) hydrogen bonds : angle 5.08876 ( 1413) covalent geometry : bond 0.00283 (13188) covalent geometry : angle 0.49272 (17940) *********************** 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 187 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.512 Fit side-chains REVERT: A 1 MET cc_start: 0.7753 (mmt) cc_final: 0.7328 (mmt) REVERT: A 111 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8465 (mm-30) REVERT: B 35 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8668 (tp40) REVERT: B 59 ARG cc_start: 0.8201 (tmt170) cc_final: 0.7783 (tpt-90) REVERT: B 61 GLN cc_start: 0.8316 (pt0) cc_final: 0.7904 (pt0) REVERT: B 111 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8468 (mm-30) REVERT: B 309 SER cc_start: 0.8790 (m) cc_final: 0.8579 (p) REVERT: B 498 ARG cc_start: 0.6940 (tpp80) cc_final: 0.6708 (ttm-80) REVERT: C 4 THR cc_start: 0.5809 (OUTLIER) cc_final: 0.5532 (t) REVERT: C 33 MET cc_start: 0.9224 (tpt) cc_final: 0.8973 (tpp) REVERT: C 61 GLN cc_start: 0.8485 (pt0) cc_final: 0.8173 (pt0) REVERT: C 354 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7581 (mptp) outliers start: 15 outliers final: 9 residues processed: 180 average time/residue: 1.6071 time to fit residues: 313.7598 Evaluate side-chains 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 175 ASP Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 70 optimal weight: 0.0000 chunk 88 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 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 = 0.3359 r_free = 0.3359 target = 0.120686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.094753 restraints weight = 28040.098| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.25 r_work: 0.2862 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1939 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= 0.098 Angle : 0.460 6.236 17940 Z= 0.249 Chirality : 0.047 0.150 2079 Planarity : 0.003 0.037 2289 Dihedral : 4.342 32.094 1773 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.73 % Allowed : 12.02 % 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: 0.42 (0.20), residues: 1614 helix: 0.25 (0.33), residues: 261 sheet: 0.70 (0.24), residues: 441 loop : 0.19 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.002 0.001 HIS A 128 PHE 0.015 0.001 BPHE B 357 TYR 0.009 0.001 TYR A 520 ARG 0.002 0.000 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 483) hydrogen bonds : angle 4.90008 ( 1413) covalent geometry : bond 0.00208 (13188) covalent geometry : angle 0.46003 (17940) ********************** 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 188 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.413 Fit side-chains REVERT: A 1 MET cc_start: 0.7808 (mmt) cc_final: 0.7338 (mmt) REVERT: A 111 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: A 203 ASN cc_start: 0.8906 (t0) cc_final: 0.8478 (t0) REVERT: B 35 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8694 (tp40) REVERT: B 59 ARG cc_start: 0.8190 (tmt170) cc_final: 0.7743 (tpt-90) REVERT: B 61 GLN cc_start: 0.8268 (pt0) cc_final: 0.7843 (pt0) REVERT: B 111 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8480 (mm-30) REVERT: B 498 ARG cc_start: 0.6939 (tpp80) cc_final: 0.6694 (ttm-80) REVERT: C 4 THR cc_start: 0.5776 (OUTLIER) cc_final: 0.5520 (t) REVERT: C 33 MET cc_start: 0.9202 (tpt) cc_final: 0.8887 (tpp) REVERT: C 61 GLN cc_start: 0.8452 (pt0) cc_final: 0.8135 (pt0) REVERT: C 374 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7962 (t0) outliers start: 11 outliers final: 4 residues processed: 182 average time/residue: 1.4050 time to fit residues: 277.2512 Evaluate side-chains 181 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 482 THR Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 374 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.0970 chunk 52 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 ASN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.094937 restraints weight = 24623.860| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.12 r_work: 0.2902 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1951 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= 0.101 Angle : 0.462 6.261 17940 Z= 0.250 Chirality : 0.047 0.150 2079 Planarity : 0.003 0.037 2289 Dihedral : 4.304 31.473 1773 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.73 % Allowed : 11.76 % 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: 0.47 (0.20), residues: 1614 helix: 0.27 (0.33), residues: 261 sheet: 0.72 (0.24), residues: 441 loop : 0.24 (0.20), residues: 912 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 PHE A 199 TYR 0.010 0.001 TYR B 520 ARG 0.002 0.000 ARG C 475 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 483) hydrogen bonds : angle 4.88455 ( 1413) covalent geometry : bond 0.00218 (13188) covalent geometry : angle 0.46213 (17940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12481.37 seconds wall clock time: 219 minutes 55.02 seconds (13195.02 seconds total)