Starting phenix.real_space_refine on Sat Sep 12 02:54:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vfd_31949/09_2026/7vfd_31949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfd_31949/09_2026/7vfd_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_31949/09_2026/7vfd_31949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfd_31949/09_2026/7vfd_31949.map" model { file = "/net/cci-nas-00/data/ceres_data/7vfd_31949/09_2026/7vfd_31949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfd_31949/09_2026/7vfd_31949.cif" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 4.13, per 1000 atoms: 0.31 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: 1.03 Conformation dependent library (CDL) restraints added in 868.9 milliseconds 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: 0.50 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: 2.33 Time building geometry restraints manager: 1.40 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.050 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.180 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (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 ARG 0.005 0.001 ARG C 412 TYR 0.011 0.002 TYR B 519 PHE 0.015 0.002 PHE C 199 TRP 0.005 0.002 TRP B 108 HIS 0.004 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (13188) covalent geometry : angle 0.53089 / 0.30 (17940) hydrogen bonds : bond 0.15596 / 10.70 ( 483) hydrogen bonds : angle 6.98135 / 4.91 ( 1413) *********************** 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 : 0.519 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: 0.6100 time to fit residues: 159.7372 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 : 0.504 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 104 ASN A 203 ASN A 223 GLN A 324 GLN B 35 GLN B 61 GLN B 104 ASN C 104 ASN C 117 ASN C 403 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.092375 restraints weight = 23072.090| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.98 r_work: 0.2790 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- 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 = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (10 function evaluations) r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1494 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= 0.192 Angle : 0.570 6.643 17940 Z= 0.314 Chirality : 0.050 0.161 2079 Planarity : 0.004 0.046 2289 Dihedral : 5.074 37.112 1776 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.40 % Allowed : 9.35 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1614 helix: -0.55 (0.30), residues: 258 sheet: 0.49 (0.22), residues: 483 loop : -0.16 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 83 TYR 0.015 0.002 TYR A 520 PHE 0.017 0.002 PHE C 199 TRP 0.015 0.002 TRP C 108 HIS 0.005 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (13188) covalent geometry : angle 0.56973 / 0.31 (17940) hydrogen bonds : bond 0.05231 / 3.53 ( 483) hydrogen bonds : angle 5.56282 / 3.84 ( 1413) *********************** 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 209 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.497 Fit side-chains REVERT: A 1 MET cc_start: 0.7877 (mmt) cc_final: 0.7388 (mmt) REVERT: A 62 TYR cc_start: 0.8336 (m-80) cc_final: 0.8048 (m-80) REVERT: A 111 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: A 204 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8368 (mtpp) REVERT: B 74 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8420 (mm-30) REVERT: B 111 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8462 (mm-30) REVERT: B 309 SER cc_start: 0.8815 (m) cc_final: 0.8508 (p) REVERT: B 486 PHE cc_start: 0.8654 (m-80) cc_final: 0.8374 (m-80) REVERT: B 539 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7020 (pt0) REVERT: C 33 MET cc_start: 0.9264 (tpt) cc_final: 0.8991 (tpp) outliers start: 21 outliers final: 8 residues processed: 201 average time/residue: 0.5914 time to fit residues: 128.7447 Evaluate side-chains 187 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 B residue 539 GLN 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 37 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 109 optimal weight: 0.0060 chunk 141 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3308 r_free = 0.3308 target = 0.116956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091013 restraints weight = 26159.649| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.17 r_work: 0.2840 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13188 Z= 0.192 Angle : 0.560 5.811 17940 Z= 0.308 Chirality : 0.050 0.155 2079 Planarity : 0.004 0.041 2289 Dihedral : 5.034 37.219 1775 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.54 % Allowed : 10.09 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1614 helix: -0.32 (0.31), residues: 261 sheet: 0.45 (0.22), residues: 483 loop : -0.12 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 290 TYR 0.015 0.002 TYR B 520 PHE 0.018 0.002 PHE C 199 TRP 0.014 0.002 TRP C 108 HIS 0.004 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (13188) covalent geometry : angle 0.55962 / 0.31 (17940) hydrogen bonds : bond 0.05121 / 3.43 ( 483) hydrogen bonds : angle 5.47595 / 3.79 ( 1413) *********************** 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 201 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.512 Fit side-chains REVERT: A 1 MET cc_start: 0.7854 (mmt) cc_final: 0.7128 (mmt) REVERT: A 111 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8550 (mm-30) REVERT: A 177 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: A 204 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8366 (mtpp) REVERT: B 35 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8559 (tp40) REVERT: B 74 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8413 (mm-30) REVERT: B 111 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8542 (mm-30) REVERT: B 309 SER cc_start: 0.8846 (m) cc_final: 0.8570 (p) REVERT: B 539 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: C 33 MET cc_start: 0.9282 (tpt) cc_final: 0.9058 (tpp) REVERT: C 61 GLN cc_start: 0.8486 (pt0) cc_final: 0.8167 (pt0) outliers start: 23 outliers final: 10 residues processed: 194 average time/residue: 0.6108 time to fit residues: 128.6453 Evaluate side-chains 189 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 177 LYS Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 81 MET 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 B residue 539 GLN Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 90 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 17 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 52 optimal weight: 7.9990 chunk 19 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN B 35 GLN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093347 restraints weight = 19876.056| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.89 r_work: 0.2808 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13188 Z= 0.156 Angle : 0.527 5.680 17940 Z= 0.289 Chirality : 0.049 0.151 2079 Planarity : 0.004 0.037 2289 Dihedral : 4.882 36.551 1775 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.27 % Allowed : 10.35 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1614 helix: -0.09 (0.32), residues: 258 sheet: 0.51 (0.22), residues: 483 loop : -0.08 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 498 TYR 0.013 0.002 TYR B 520 PHE 0.016 0.002 PHE C 199 TRP 0.012 0.002 TRP C 108 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (13188) covalent geometry : angle 0.52740 / 0.29 (17940) hydrogen bonds : bond 0.04636 / 3.10 ( 483) hydrogen bonds : angle 5.33629 / 3.69 ( 1413) *********************** 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 194 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.534 Fit side-chains REVERT: A 1 MET cc_start: 0.7770 (mmt) cc_final: 0.7289 (mmt) REVERT: A 111 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8487 (mm-30) REVERT: B 111 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8458 (mm-30) REVERT: B 309 SER cc_start: 0.8809 (m) cc_final: 0.8554 (p) REVERT: C 33 MET cc_start: 0.9243 (tpt) cc_final: 0.8998 (tpp) REVERT: C 61 GLN cc_start: 0.8441 (pt0) cc_final: 0.8115 (pt0) REVERT: C 354 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7415 (mptp) REVERT: C 374 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7998 (t0) REVERT: C 436 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8414 (tmtp) outliers start: 19 outliers final: 8 residues processed: 185 average time/residue: 0.6086 time to fit residues: 122.1531 Evaluate side-chains 186 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 81 MET 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 90 VAL Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 436 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 131 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.8514 > 50:) chunk 68 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN B 35 GLN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.090776 restraints weight = 30427.481| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.33 r_work: 0.2833 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1718 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= 0.173 Angle : 0.540 5.798 17940 Z= 0.297 Chirality : 0.050 0.151 2079 Planarity : 0.004 0.039 2289 Dihedral : 4.928 36.593 1775 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.74 % Allowed : 10.22 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1614 helix: -0.10 (0.31), residues: 261 sheet: 0.46 (0.22), residues: 486 loop : -0.06 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 498 TYR 0.015 0.002 TYR B 520 PHE 0.017 0.002 PHE C 199 TRP 0.011 0.002 TRP C 108 HIS 0.004 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13188) covalent geometry : angle 0.54012 / 0.30 (17940) hydrogen bonds : bond 0.04824 / 3.23 ( 483) hydrogen bonds : angle 5.38579 / 3.73 ( 1413) *********************** 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 206 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.515 Fit side-chains REVERT: A 1 MET cc_start: 0.7860 (mmt) cc_final: 0.7348 (mmt) REVERT: A 111 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8573 (mm-30) REVERT: A 204 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8357 (mtpp) REVERT: B 111 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8527 (mm-30) REVERT: B 146 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: B 309 SER cc_start: 0.8869 (m) cc_final: 0.8638 (p) REVERT: B 353 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7642 (mtp-110) REVERT: C 33 MET cc_start: 0.9287 (tpt) cc_final: 0.9053 (tpp) REVERT: C 61 GLN cc_start: 0.8486 (pt0) cc_final: 0.8179 (pt0) REVERT: C 436 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8466 (tmtp) outliers start: 26 outliers final: 12 residues processed: 194 average time/residue: 0.6300 time to fit residues: 132.1614 Evaluate side-chains 193 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 81 MET 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 175 ASP Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 436 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 25 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 87 optimal weight: 0.0770 chunk 102 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3305 r_free = 0.3305 target = 0.116712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.091504 restraints weight = 23294.131| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.04 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13188 Z= 0.207 Angle : 0.578 6.539 17940 Z= 0.318 Chirality : 0.051 0.151 2079 Planarity : 0.004 0.045 2289 Dihedral : 5.060 37.073 1775 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.40 % Allowed : 10.69 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 1614 helix: -0.13 (0.31), residues: 258 sheet: 0.47 (0.22), residues: 483 loop : -0.13 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 498 TYR 0.018 0.002 TYR B 520 PHE 0.019 0.002 PHE C 199 TRP 0.011 0.002 TRP C 108 HIS 0.004 0.002 HIS B 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (13188) covalent geometry : angle 0.57835 / 0.32 (17940) hydrogen bonds : bond 0.05155 / 3.45 ( 483) hydrogen bonds : angle 5.50400 / 3.81 ( 1413) *********************** 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 199 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.511 Fit side-chains REVERT: A 1 MET cc_start: 0.7817 (mmt) cc_final: 0.7352 (mmt) REVERT: A 111 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8523 (mm-30) REVERT: A 204 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8355 (mtpp) REVERT: B 61 GLN cc_start: 0.8362 (pt0) cc_final: 0.7946 (pt0) REVERT: B 111 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8533 (mm-30) REVERT: B 309 SER cc_start: 0.8852 (m) cc_final: 0.8609 (p) REVERT: B 353 ARG cc_start: 0.7928 (mtm-85) cc_final: 0.7638 (mtp-110) REVERT: C 33 MET cc_start: 0.9293 (tpt) cc_final: 0.9058 (tpp) REVERT: C 61 GLN cc_start: 0.8467 (pt0) cc_final: 0.8151 (pt0) REVERT: C 353 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7645 (mtp-110) REVERT: C 354 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7347 (mptp) REVERT: C 436 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8477 (tmtp) outliers start: 21 outliers final: 13 residues processed: 187 average time/residue: 0.6409 time to fit residues: 129.6269 Evaluate side-chains 193 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain B residue 81 MET 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 204 LYS Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 436 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 77 optimal weight: 0.0070 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3308 r_free = 0.3308 target = 0.116998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.091599 restraints weight = 27692.231| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.14 r_work: 0.2785 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13188 Z= 0.145 Angle : 0.511 6.126 17940 Z= 0.280 Chirality : 0.049 0.150 2079 Planarity : 0.004 0.037 2289 Dihedral : 4.798 36.092 1775 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.20 % Allowed : 10.96 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1614 helix: -0.02 (0.32), residues: 261 sheet: 0.55 (0.23), residues: 483 loop : -0.03 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 498 TYR 0.013 0.002 TYR B 520 PHE 0.017 0.002 PHE A 199 TRP 0.010 0.002 TRP B 108 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (13188) covalent geometry : angle 0.51143 / 0.28 (17940) hydrogen bonds : bond 0.04399 / 2.93 ( 483) hydrogen bonds : angle 5.27921 / 3.65 ( 1413) *********************** 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 191 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.532 Fit side-chains REVERT: A 1 MET cc_start: 0.7806 (mmt) cc_final: 0.7328 (mmt) REVERT: A 111 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8546 (mm-30) REVERT: B 61 GLN cc_start: 0.8313 (pt0) cc_final: 0.7905 (pt0) REVERT: B 111 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8490 (mm-30) REVERT: B 309 SER cc_start: 0.8840 (m) cc_final: 0.8587 (p) REVERT: C 33 MET cc_start: 0.9272 (tpt) cc_final: 0.9029 (tpp) REVERT: C 61 GLN cc_start: 0.8527 (pt0) cc_final: 0.8211 (pt0) REVERT: C 354 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7447 (mptp) REVERT: C 374 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.8005 (t0) REVERT: C 436 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8431 (tmtp) outliers start: 18 outliers final: 9 residues processed: 178 average time/residue: 0.6201 time to fit residues: 119.6384 Evaluate side-chains 184 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 B residue 24 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 436 LYS 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 124 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3322 r_free = 0.3322 target = 0.117923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.091531 restraints weight = 29583.007| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.30 r_work: 0.2847 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13188 Z= 0.149 Angle : 0.520 6.617 17940 Z= 0.284 Chirality : 0.049 0.149 2079 Planarity : 0.004 0.038 2289 Dihedral : 4.804 35.567 1775 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.27 % Allowed : 10.75 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1614 helix: 0.03 (0.32), residues: 261 sheet: 0.55 (0.23), residues: 483 loop : 0.00 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 498 TYR 0.013 0.002 TYR B 520 PHE 0.017 0.002 PHE A 199 TRP 0.011 0.002 TRP C 108 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (13188) covalent geometry : angle 0.51995 / 0.28 (17940) hydrogen bonds : bond 0.04463 / 2.98 ( 483) hydrogen bonds : angle 5.28775 / 3.66 ( 1413) *********************** 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 191 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.525 Fit side-chains REVERT: A 1 MET cc_start: 0.7851 (mmt) cc_final: 0.7361 (mmt) REVERT: A 111 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8565 (mm-30) REVERT: B 61 GLN cc_start: 0.8332 (pt0) cc_final: 0.7913 (pt0) REVERT: B 111 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8546 (mm-30) REVERT: B 309 SER cc_start: 0.8852 (m) cc_final: 0.8621 (p) REVERT: B 512 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8154 (mtt) REVERT: C 33 MET cc_start: 0.9281 (tpt) cc_final: 0.9047 (tpp) REVERT: C 61 GLN cc_start: 0.8533 (pt0) cc_final: 0.8229 (pt0) REVERT: C 354 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7477 (mptp) REVERT: C 374 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8054 (t0) REVERT: C 436 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8459 (tmtp) outliers start: 19 outliers final: 11 residues processed: 178 average time/residue: 0.6293 time to fit residues: 121.5442 Evaluate side-chains 188 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain B residue 81 MET 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 204 LYS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 436 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 138 optimal weight: 0.0980 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3317 r_free = 0.3317 target = 0.117693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.092700 restraints weight = 26147.702| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.08 r_work: 0.2804 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13188 Z= 0.130 Angle : 0.498 6.303 17940 Z= 0.272 Chirality : 0.048 0.150 2079 Planarity : 0.003 0.037 2289 Dihedral : 4.688 34.820 1775 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.07 % Allowed : 11.22 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1614 helix: 0.09 (0.32), residues: 261 sheet: 0.62 (0.23), residues: 480 loop : 0.03 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 498 TYR 0.012 0.002 TYR B 520 PHE 0.016 0.002 PHE A 199 TRP 0.011 0.002 TRP B 108 HIS 0.002 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13188) covalent geometry : angle 0.49765 / 0.27 (17940) hydrogen bonds : bond 0.04170 / 2.77 ( 483) hydrogen bonds : angle 5.19561 / 3.59 ( 1413) *********************** 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: 16 poor density : 171 time to evaluate : 0.526 Fit side-chains REVERT: A 1 MET cc_start: 0.7774 (mmt) cc_final: 0.7307 (mmt) REVERT: A 111 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8542 (mm-30) REVERT: B 59 ARG cc_start: 0.8167 (tmt170) cc_final: 0.7774 (tpt-90) REVERT: B 61 GLN cc_start: 0.8271 (pt0) cc_final: 0.7856 (pt0) REVERT: B 111 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8477 (mm-30) REVERT: B 309 SER cc_start: 0.8838 (m) cc_final: 0.8596 (p) REVERT: C 33 MET cc_start: 0.9266 (tpt) cc_final: 0.9025 (tpp) REVERT: C 61 GLN cc_start: 0.8509 (pt0) cc_final: 0.8196 (pt0) REVERT: C 354 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7529 (mptp) REVERT: C 374 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7986 (t0) REVERT: C 436 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8437 (tmtp) outliers start: 16 outliers final: 9 residues processed: 177 average time/residue: 0.6084 time to fit residues: 116.8367 Evaluate side-chains 183 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 81 MET 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 204 LYS Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 436 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 51 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 122 optimal weight: 0.0970 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.117396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091066 restraints weight = 31632.198| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.45 r_work: 0.2776 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13188 Z= 0.149 Angle : 0.519 6.744 17940 Z= 0.284 Chirality : 0.049 0.149 2079 Planarity : 0.004 0.038 2289 Dihedral : 4.761 35.132 1775 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.07 % Allowed : 10.96 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1614 helix: 0.09 (0.32), residues: 261 sheet: 0.56 (0.23), residues: 483 loop : 0.05 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 498 TYR 0.014 0.002 TYR B 520 PHE 0.017 0.002 PHE A 199 TRP 0.011 0.002 TRP C 108 HIS 0.003 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13188) covalent geometry : angle 0.51912 / 0.28 (17940) hydrogen bonds : bond 0.04436 / 2.96 ( 483) hydrogen bonds : angle 5.25887 / 3.64 ( 1413) ********************** 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 189 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.505 Fit side-chains REVERT: A 1 MET cc_start: 0.7798 (mmt) cc_final: 0.7305 (mmt) REVERT: A 111 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (mm-30) REVERT: B 59 ARG cc_start: 0.8224 (tmt170) cc_final: 0.7792 (tpt-90) REVERT: B 61 GLN cc_start: 0.8283 (pt0) cc_final: 0.7861 (pt0) REVERT: B 111 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8561 (mm-30) REVERT: B 309 SER cc_start: 0.8843 (m) cc_final: 0.8595 (p) REVERT: B 353 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7591 (mtp-110) REVERT: B 512 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8147 (mtt) REVERT: C 33 MET cc_start: 0.9296 (tpt) cc_final: 0.9064 (tpp) REVERT: C 61 GLN cc_start: 0.8535 (pt0) cc_final: 0.8239 (pt0) REVERT: C 354 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7553 (mptp) REVERT: C 374 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8065 (t0) REVERT: C 436 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8447 (tmtp) outliers start: 16 outliers final: 9 residues processed: 178 average time/residue: 0.6348 time to fit residues: 122.1916 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 : 0.463 ------------------------------------------------------------------------------- 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 24 VAL Chi-restraints excluded: chain B residue 81 MET 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 482 THR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 354 LYS Chi-restraints excluded: chain C residue 374 ASP Chi-restraints excluded: chain C residue 436 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN C 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.119326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.095620 restraints weight = 18276.531| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.80 r_work: 0.2878 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1895 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= 0.113 Angle : 0.481 6.266 17940 Z= 0.261 Chirality : 0.047 0.151 2079 Planarity : 0.003 0.036 2289 Dihedral : 4.543 33.593 1775 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.87 % Allowed : 11.42 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1614 helix: 0.16 (0.33), residues: 261 sheet: 0.61 (0.23), residues: 483 loop : 0.11 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 498 TYR 0.010 0.001 TYR B 520 PHE 0.015 0.001 PHE A 199 TRP 0.011 0.002 TRP B 108 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (13188) covalent geometry : angle 0.48071 / 0.26 (17940) hydrogen bonds : bond 0.03879 / 2.57 ( 483) hydrogen bonds : angle 5.08860 / 3.51 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5321.17 seconds wall clock time: 91 minutes 20.75 seconds (5480.75 seconds total)