Starting phenix.real_space_refine on Sat Sep 12 02:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9usz_64476/09_2026/9usz_64476.cif Found real_map, /net/cci-nas-00/data/ceres_data/9usz_64476/09_2026/9usz_64476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9usz_64476/09_2026/9usz_64476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9usz_64476/09_2026/9usz_64476.map" model { file = "/net/cci-nas-00/data/ceres_data/9usz_64476/09_2026/9usz_64476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9usz_64476/09_2026/9usz_64476.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 2520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 12912 Number of models: 1 Model: "" Number of chains: 3 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 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ACYS A 94 " occ=0.28 ... (10 atoms not shown) pdb=" SG BCYS A 94 " occ=0.72 residue: pdb=" N ACYS B 94 " occ=0.44 ... (10 atoms not shown) pdb=" SG BCYS B 94 " occ=0.56 residue: pdb=" N ACYS C 94 " occ=0.60 ... (10 atoms not shown) pdb=" SG BCYS C 94 " occ=0.40 Time building chain proxies: 5.63, per 1000 atoms: 0.44 Number of scatterers: 12912 At special positions: 0 Unit cell: (98.01, 96.228, 109.296, 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 2520 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 1.0 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 36 sheets defined 20.1% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 3.919A 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 119 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.010A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.680A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.804A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.621A 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: 4.068A 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: 4.003A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 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: 3.884A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.530A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.961A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.714A 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: 4.035A 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: 3.879A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (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: 3.894A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.512A pdb=" N THR C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.917A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.725A 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: 4.226A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.093A 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: 4.226A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.927A 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: 6.753A pdb=" N ASN A 96 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLU A 111 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 98 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU A 109 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 100 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.537A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) 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: 3.890A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.676A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 3.890A 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: 6.710A pdb=" N SER A 504 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A 445 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG A 506 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU A 443 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 508 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.619A 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: 6.674A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 6.929A 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: 4.180A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.224A 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: 4.180A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.949A 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: 6.070A pdb=" N SER B 102 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.161A 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 removed outlier: 6.555A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) 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 239 removed outlier: 4.801A pdb=" N LEU B 525 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE B 239 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS B 523 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.573A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 4.130A 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 247 removed outlier: 6.533A pdb=" N LYS B 502 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE B 447 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER B 504 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 445 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ARG B 506 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU B 443 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 508 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 443 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B 454 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 445 " --> pdb=" O LEU B 452 " (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: 5.062A pdb=" N SER B 366 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 6.983A 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: 4.010A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.227A 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: 4.010A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.743A 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: 6.882A pdb=" N ASN C 96 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU C 111 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 98 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU C 109 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 100 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.545A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) 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: 3.837A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.732A 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: 3.644A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.837A 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 247 removed outlier: 6.325A pdb=" N LYS C 502 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C 447 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER C 504 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 445 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG C 506 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 443 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 508 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 443 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 454 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 445 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 450 " --> 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: 6.674A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE C 365 " --> pdb=" O HIS C 386 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N HIS C 386 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 367 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 384 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 6.922A 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 350 520 hydrogen bonds defined for protein. 1362 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: 2.76 Time building geometry restraints manager: 1.46 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: 4049 1.34 - 1.45: 1993 1.45 - 1.57: 7077 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 13188 Sorted by residual: bond pdb=" N LYS B 429 " pdb=" CA LYS B 429 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.49e+00 bond pdb=" N ILE B 431 " pdb=" CA ILE B 431 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.02e+00 bond pdb=" N LEU C 347 " pdb=" CA LEU C 347 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.30e+00 bond pdb=" N ASP B 432 " pdb=" CA ASP B 432 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.93e+00 bond pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.45e+00 ... (remaining 13183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 17258 1.18 - 2.36: 541 2.36 - 3.54: 126 3.54 - 4.72: 12 4.72 - 5.90: 3 Bond angle restraints: 17940 Sorted by residual: angle pdb=" N ILE A 431 " pdb=" CA ILE A 431 " pdb=" C ILE A 431 " ideal model delta sigma weight residual 113.20 109.71 3.49 9.60e-01 1.09e+00 1.32e+01 angle pdb=" CA ASN C 334 " pdb=" CB ASN C 334 " pdb=" CG ASN C 334 " ideal model delta sigma weight residual 112.60 115.68 -3.08 1.00e+00 1.00e+00 9.47e+00 angle pdb=" N ILE C 431 " pdb=" CA ILE C 431 " pdb=" C ILE C 431 " ideal model delta sigma weight residual 113.20 110.38 2.82 9.60e-01 1.09e+00 8.64e+00 angle pdb=" CA GLY B 430 " pdb=" C GLY B 430 " pdb=" O GLY B 430 " ideal model delta sigma weight residual 121.67 118.14 3.53 1.24e+00 6.50e-01 8.08e+00 angle pdb=" CA LYS B 429 " pdb=" C LYS B 429 " pdb=" O LYS B 429 " ideal model delta sigma weight residual 121.46 118.14 3.32 1.17e+00 7.31e-01 8.05e+00 ... (remaining 17935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7155 17.96 - 35.93: 569 35.93 - 53.89: 150 53.89 - 71.85: 41 71.85 - 89.81: 20 Dihedral angle restraints: 7935 sinusoidal: 3117 harmonic: 4818 Sorted by residual: dihedral pdb=" CA ASP C 327 " pdb=" CB ASP C 327 " pdb=" CG ASP C 327 " pdb=" OD1 ASP C 327 " ideal model delta sinusoidal sigma weight residual -30.00 -88.18 58.18 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU A 415 " pdb=" CG GLU A 415 " pdb=" CD GLU A 415 " pdb=" OE1 GLU A 415 " ideal model delta sinusoidal sigma weight residual 0.00 88.59 -88.59 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU C 314 " pdb=" CG GLU C 314 " pdb=" CD GLU C 314 " pdb=" OE1 GLU C 314 " ideal model delta sinusoidal sigma weight residual 0.00 85.43 -85.43 1 3.00e+01 1.11e-03 9.82e+00 ... (remaining 7932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1406 0.039 - 0.078: 412 0.078 - 0.117: 231 0.117 - 0.156: 29 0.156 - 0.195: 1 Chirality restraints: 2079 Sorted by residual: chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA LEU C 348 " pdb=" N LEU C 348 " pdb=" C LEU C 348 " pdb=" CB LEU C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 2076 not shown) Planarity restraints: 2289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 334 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C ASN C 334 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN C 334 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL C 335 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 519 " -0.010 2.00e-02 2.50e+03 1.17e-02 2.73e+00 pdb=" CG TYR C 519 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR C 519 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 519 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 519 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 519 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 519 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 519 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 203 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" CG ASN C 203 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 203 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 203 " -0.009 2.00e-02 2.50e+03 ... (remaining 2286 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 708 2.73 - 3.28: 12239 3.28 - 3.82: 21654 3.82 - 4.36: 27444 4.36 - 4.90: 46665 Nonbonded interactions: 108710 Sorted by model distance: nonbonded pdb=" OH TYR B 359 " pdb=" OD1 ASP B 392 " model vdw 2.192 3.040 nonbonded pdb=" OE1 GLU B 74 " pdb=" OG1 THR B 153 " model vdw 2.205 3.040 nonbonded pdb=" OG SER B 72 " pdb=" OE1 GLU B 211 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OD1 ASP A 392 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP A 267 " pdb=" OG SER A 398 " model vdw 2.249 3.040 ... (remaining 108705 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'B' and (resid 0 through 93 or resid 95 through 356 or resid 358 through \ 547)) selection = (chain 'C' and (resid 0 through 93 or resid 95 through 356 or resid 358 through \ 547)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.28 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.110 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 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 0.047 13188 Z= 0.177 Angle : 0.525 5.899 17940 Z= 0.305 Chirality : 0.047 0.195 2079 Planarity : 0.004 0.032 2289 Dihedral : 15.287 89.814 4833 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % 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: 0.41 (0.21), residues: 1614 helix: -0.01 (0.33), residues: 255 sheet: 0.97 (0.24), residues: 492 loop : 0.04 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 234 TYR 0.029 0.002 TYR C 519 PHE 0.017 0.002 PHE C 381 TRP 0.005 0.001 TRP B 400 HIS 0.003 0.001 HIS A 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (13188) covalent geometry : angle 0.52485 / 0.31 (17940) hydrogen bonds : bond 0.15968 / 10.37 ( 460) hydrogen bonds : angle 7.10094 / 4.93 ( 1362) *********************** 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 196 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.536 Fit side-chains REVERT: C 146 ASP cc_start: 0.7802 (t70) cc_final: 0.7519 (t70) REVERT: C 334 ASN cc_start: 0.7499 (t0) cc_final: 0.7222 (t0) outliers start: 0 outliers final: 1 residues processed: 196 average time/residue: 0.5914 time to fit residues: 127.1268 Evaluate side-chains 175 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN B 334 ASN C 50 ASN C 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107305 restraints weight = 28334.124| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.75 r_work: 0.3154 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13188 Z= 0.228 Angle : 0.555 6.953 17940 Z= 0.298 Chirality : 0.050 0.155 2079 Planarity : 0.004 0.041 2289 Dihedral : 4.541 25.760 1772 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.61 % Allowed : 12.76 % Favored : 83.63 % 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: 0.26 (0.20), residues: 1614 helix: -0.14 (0.32), residues: 252 sheet: 0.79 (0.25), residues: 420 loop : 0.07 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 234 TYR 0.014 0.002 TYR B 359 PHE 0.019 0.002 PHE C 381 TRP 0.006 0.002 TRP B 108 HIS 0.004 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (13188) covalent geometry : angle 0.55535 / 0.30 (17940) hydrogen bonds : bond 0.04793 / 3.07 ( 460) hydrogen bonds : angle 5.41993 / 3.79 ( 1362) *********************** 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 240 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.652 Fit side-chains REVERT: A 547 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7377 (mtt) REVERT: C 150 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: C 547 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7234 (mtt) outliers start: 53 outliers final: 27 residues processed: 209 average time/residue: 0.5657 time to fit residues: 130.2097 Evaluate side-chains 207 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 104 ASN B 334 ASN C 50 ASN C 203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106405 restraints weight = 25573.691| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.78 r_work: 0.3037 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13188 Z= 0.141 Angle : 0.475 6.087 17940 Z= 0.256 Chirality : 0.048 0.152 2079 Planarity : 0.004 0.036 2289 Dihedral : 4.260 23.958 1772 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 14.16 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.20), residues: 1614 helix: -0.01 (0.33), residues: 255 sheet: 0.78 (0.25), residues: 417 loop : 0.13 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.013 0.001 TYR B 359 PHE 0.013 0.001 PHE C 199 TRP 0.005 0.001 TRP B 108 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (13188) covalent geometry : angle 0.47518 / 0.26 (17940) hydrogen bonds : bond 0.03856 / 2.47 ( 460) hydrogen bonds : angle 5.08501 / 3.54 ( 1362) *********************** 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 232 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.539 Fit side-chains REVERT: A 444 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 547 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7084 (mtt) REVERT: B 493 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8450 (p) REVERT: C 150 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: C 175 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7623 (t0) REVERT: C 547 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7015 (mtt) outliers start: 40 outliers final: 18 residues processed: 206 average time/residue: 0.5766 time to fit residues: 130.3189 Evaluate side-chains 209 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN B 104 ASN B 334 ASN C 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.132178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107109 restraints weight = 26157.536| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.66 r_work: 0.3161 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13188 Z= 0.239 Angle : 0.559 9.849 17940 Z= 0.297 Chirality : 0.050 0.151 2079 Planarity : 0.004 0.038 2289 Dihedral : 4.563 18.102 1770 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.61 % Allowed : 13.49 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1614 helix: -0.18 (0.32), residues: 252 sheet: 0.71 (0.25), residues: 411 loop : -0.01 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 234 TYR 0.016 0.002 TYR B 359 PHE 0.018 0.002 PHE C 199 TRP 0.006 0.002 TRP B 400 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (13188) covalent geometry : angle 0.55882 / 0.30 (17940) hydrogen bonds : bond 0.04565 / 2.92 ( 460) hydrogen bonds : angle 5.28260 / 3.69 ( 1362) *********************** 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 234 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.525 Fit side-chains REVERT: A 311 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7407 (mm-30) REVERT: A 444 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: A 547 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7376 (mtt) REVERT: B 512 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6995 (mtp) REVERT: C 59 ARG cc_start: 0.8274 (tpt90) cc_final: 0.7868 (tpt90) REVERT: C 150 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: C 404 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7536 (ptp90) REVERT: C 547 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7332 (mtt) outliers start: 53 outliers final: 34 residues processed: 208 average time/residue: 0.5560 time to fit residues: 126.8927 Evaluate side-chains 218 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 484 LYS Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 0.0030 chunk 47 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 495 ASN B 104 ASN B 121 ASN B 334 ASN C 50 ASN C 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106767 restraints weight = 32718.610| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.39 r_work: 0.3029 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13188 Z= 0.105 Angle : 0.452 9.222 17940 Z= 0.242 Chirality : 0.047 0.153 2079 Planarity : 0.004 0.035 2289 Dihedral : 4.052 17.738 1770 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.74 % Allowed : 14.83 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1614 helix: -0.07 (0.33), residues: 264 sheet: 0.76 (0.25), residues: 411 loop : 0.20 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 83 TYR 0.013 0.001 TYR B 359 PHE 0.009 0.001 PHE C 199 TRP 0.004 0.001 TRP B 400 HIS 0.002 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (13188) covalent geometry : angle 0.45154 / 0.24 (17940) hydrogen bonds : bond 0.03289 / 2.11 ( 460) hydrogen bonds : angle 4.88453 / 3.41 ( 1362) *********************** 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 227 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.442 Fit side-chains REVERT: A 324 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: A 377 LYS cc_start: 0.7969 (mptp) cc_final: 0.7471 (mtmt) REVERT: A 547 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7083 (mtt) REVERT: B 218 MET cc_start: 0.8814 (ttp) cc_final: 0.8582 (ttp) REVERT: B 317 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: B 444 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: B 493 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8381 (p) REVERT: C 59 ARG cc_start: 0.8153 (tpt90) cc_final: 0.7692 (tpt90) REVERT: C 146 ASP cc_start: 0.7849 (t70) cc_final: 0.7560 (t70) REVERT: C 150 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 334 ASN cc_start: 0.7329 (t0) cc_final: 0.7068 (t0) REVERT: C 547 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7121 (mmt) outliers start: 39 outliers final: 21 residues processed: 206 average time/residue: 0.5483 time to fit residues: 124.3546 Evaluate side-chains 209 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 GLN A 495 ASN B 104 ASN B 334 ASN C 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107750 restraints weight = 22302.859| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.60 r_work: 0.3058 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13188 Z= 0.133 Angle : 0.472 8.922 17940 Z= 0.251 Chirality : 0.047 0.152 2079 Planarity : 0.004 0.034 2289 Dihedral : 4.104 17.877 1770 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.94 % Allowed : 14.63 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1614 helix: 0.02 (0.33), residues: 261 sheet: 0.75 (0.25), residues: 411 loop : 0.20 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 404 TYR 0.013 0.001 TYR B 359 PHE 0.013 0.001 PHE C 199 TRP 0.004 0.001 TRP B 400 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (13188) covalent geometry : angle 0.47172 / 0.25 (17940) hydrogen bonds : bond 0.03524 / 2.26 ( 460) hydrogen bonds : angle 4.90924 / 3.43 ( 1362) *********************** 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 222 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.765 Fit side-chains REVERT: A 324 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: A 444 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: A 547 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7189 (mtt) REVERT: B 218 MET cc_start: 0.8934 (ttp) cc_final: 0.8733 (ttp) REVERT: B 317 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: B 374 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6753 (t0) REVERT: C 59 ARG cc_start: 0.8233 (tpt90) cc_final: 0.7754 (tpt90) REVERT: C 150 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 175 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: C 404 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7425 (ptp90) REVERT: C 547 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7112 (mtt) outliers start: 42 outliers final: 24 residues processed: 202 average time/residue: 0.5542 time to fit residues: 123.3952 Evaluate side-chains 212 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 69 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 HIS A 495 ASN B 104 ASN B 334 ASN C 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.107039 restraints weight = 23427.652| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.66 r_work: 0.3045 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13188 Z= 0.144 Angle : 0.480 8.730 17940 Z= 0.256 Chirality : 0.047 0.150 2079 Planarity : 0.004 0.035 2289 Dihedral : 4.156 17.742 1770 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.01 % Allowed : 14.83 % Favored : 82.16 % 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: 0.40 (0.21), residues: 1614 helix: 0.13 (0.34), residues: 252 sheet: 0.84 (0.24), residues: 441 loop : 0.12 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.014 0.001 TYR B 359 PHE 0.014 0.001 PHE C 199 TRP 0.004 0.001 TRP B 400 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (13188) covalent geometry : angle 0.48026 / 0.26 (17940) hydrogen bonds : bond 0.03616 / 2.32 ( 460) hydrogen bonds : angle 4.95066 / 3.45 ( 1362) *********************** 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 223 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.378 Fit side-chains REVERT: A 324 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: A 444 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: A 547 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7095 (mtt) REVERT: B 218 MET cc_start: 0.8819 (ttp) cc_final: 0.8592 (ttp) REVERT: B 317 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 354 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6164 (mmtm) REVERT: B 374 ASP cc_start: 0.6906 (t0) cc_final: 0.6628 (t0) REVERT: B 444 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: B 493 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8431 (p) REVERT: C 59 ARG cc_start: 0.8119 (tpt90) cc_final: 0.7685 (tpt90) REVERT: C 150 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 175 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7711 (m-30) REVERT: C 311 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: C 334 ASN cc_start: 0.7383 (t0) cc_final: 0.7100 (t0) REVERT: C 404 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7327 (ptp90) REVERT: C 484 LYS cc_start: 0.8703 (mtpp) cc_final: 0.7976 (mmtm) REVERT: C 547 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7165 (mmt) outliers start: 43 outliers final: 28 residues processed: 206 average time/residue: 0.5654 time to fit residues: 128.0780 Evaluate side-chains 224 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 404 ARG Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 141 optimal weight: 0.0000 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 122 optimal weight: 0.0060 chunk 151 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 104 ASN B 334 ASN C 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107449 restraints weight = 31576.826| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.17 r_work: 0.3046 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13188 Z= 0.099 Angle : 0.440 8.544 17940 Z= 0.235 Chirality : 0.046 0.151 2079 Planarity : 0.003 0.034 2289 Dihedral : 3.887 17.497 1770 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.74 % Allowed : 15.03 % Favored : 82.23 % 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: 0.50 (0.21), residues: 1614 helix: 0.04 (0.33), residues: 264 sheet: 0.89 (0.24), residues: 441 loop : 0.25 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.012 0.001 TYR B 359 PHE 0.010 0.001 PHE C 199 TRP 0.004 0.001 TRP B 108 HIS 0.002 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (13188) covalent geometry : angle 0.43988 / 0.24 (17940) hydrogen bonds : bond 0.03083 / 1.98 ( 460) hydrogen bonds : angle 4.73475 / 3.30 ( 1362) *********************** 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 228 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.571 Fit side-chains REVERT: A 1 MET cc_start: 0.5659 (OUTLIER) cc_final: 0.4845 (tpt) REVERT: A 285 ASP cc_start: 0.7859 (m-30) cc_final: 0.7410 (m-30) REVERT: A 324 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: A 377 LYS cc_start: 0.8073 (mptp) cc_final: 0.7557 (mtmt) REVERT: B 218 MET cc_start: 0.8811 (ttp) cc_final: 0.8608 (ttp) REVERT: B 317 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 354 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6099 (mmtm) REVERT: B 374 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6555 (t0) REVERT: B 444 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: B 493 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8389 (p) REVERT: C 59 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7713 (tpt90) REVERT: C 150 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 175 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: C 311 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7784 (mt-10) REVERT: C 334 ASN cc_start: 0.7369 (t0) cc_final: 0.7083 (t0) REVERT: C 547 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7151 (mmt) outliers start: 39 outliers final: 22 residues processed: 210 average time/residue: 0.5800 time to fit residues: 133.6550 Evaluate side-chains 210 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 132 optimal weight: 0.0770 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 ASN B 104 ASN B 334 ASN C 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108572 restraints weight = 29018.157| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.90 r_work: 0.3060 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13188 Z= 0.099 Angle : 0.439 8.490 17940 Z= 0.235 Chirality : 0.046 0.152 2079 Planarity : 0.003 0.035 2289 Dihedral : 3.837 17.227 1770 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.14 % Allowed : 15.76 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.53 (0.21), residues: 1614 helix: 0.10 (0.33), residues: 264 sheet: 0.87 (0.24), residues: 441 loop : 0.29 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.011 0.001 TYR B 359 PHE 0.010 0.001 PHE C 199 TRP 0.004 0.001 TRP B 108 HIS 0.002 0.000 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (13188) covalent geometry : angle 0.43943 / 0.23 (17940) hydrogen bonds : bond 0.03075 / 1.98 ( 460) hydrogen bonds : angle 4.68064 / 3.27 ( 1362) *********************** 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 212 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.527 Fit side-chains REVERT: A 285 ASP cc_start: 0.7860 (m-30) cc_final: 0.7418 (m-30) REVERT: A 324 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: B 218 MET cc_start: 0.8801 (ttp) cc_final: 0.8596 (ttp) REVERT: B 317 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: B 354 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6160 (mmtm) REVERT: B 374 ASP cc_start: 0.6774 (t0) cc_final: 0.6493 (t0) REVERT: B 444 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: C 59 ARG cc_start: 0.8147 (tpt90) cc_final: 0.7705 (tpt90) REVERT: C 150 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 175 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: C 334 ASN cc_start: 0.7361 (t0) cc_final: 0.7105 (t0) REVERT: C 547 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7149 (mmt) outliers start: 30 outliers final: 24 residues processed: 201 average time/residue: 0.5560 time to fit residues: 123.3443 Evaluate side-chains 209 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 93 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 105 optimal weight: 0.1980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 104 ASN B 334 ASN C 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.107126 restraints weight = 23324.732| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.67 r_work: 0.3048 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13188 Z= 0.149 Angle : 0.483 8.451 17940 Z= 0.257 Chirality : 0.048 0.150 2079 Planarity : 0.004 0.036 2289 Dihedral : 4.114 17.470 1770 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.34 % Allowed : 15.76 % Favored : 81.90 % 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: 0.43 (0.21), residues: 1614 helix: 0.03 (0.33), residues: 261 sheet: 0.84 (0.24), residues: 441 loop : 0.20 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.013 0.001 TYR B 359 PHE 0.014 0.002 PHE C 199 TRP 0.004 0.001 TRP B 400 HIS 0.003 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13188) covalent geometry : angle 0.48348 / 0.26 (17940) hydrogen bonds : bond 0.03624 / 2.33 ( 460) hydrogen bonds : angle 4.89716 / 3.42 ( 1362) ********************** 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 210 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.526 Fit side-chains REVERT: A 324 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: A 444 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: B 317 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: B 354 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6132 (mmtm) REVERT: B 374 ASP cc_start: 0.6969 (t0) cc_final: 0.6705 (t0) REVERT: B 444 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: C 59 ARG cc_start: 0.8245 (tpt90) cc_final: 0.7763 (tpt90) REVERT: C 150 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: C 175 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: C 334 ASN cc_start: 0.7439 (t0) cc_final: 0.7153 (t0) REVERT: C 547 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7238 (mmt) outliers start: 33 outliers final: 24 residues processed: 198 average time/residue: 0.5605 time to fit residues: 122.1299 Evaluate side-chains 206 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 403 GLN Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 547 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 58 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN B 104 ASN B 334 ASN C 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106618 restraints weight = 29197.660| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.99 r_work: 0.3034 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1128 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= 0.131 Angle : 0.469 8.432 17940 Z= 0.250 Chirality : 0.047 0.151 2079 Planarity : 0.004 0.035 2289 Dihedral : 4.056 17.202 1770 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.47 % Allowed : 15.76 % Favored : 81.76 % 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: 0.44 (0.21), residues: 1614 helix: -0.04 (0.33), residues: 264 sheet: 0.83 (0.24), residues: 441 loop : 0.24 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 404 TYR 0.013 0.001 TYR B 359 PHE 0.013 0.001 PHE C 199 TRP 0.004 0.001 TRP B 400 HIS 0.002 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (13188) covalent geometry : angle 0.46899 / 0.25 (17940) hydrogen bonds : bond 0.03439 / 2.21 ( 460) hydrogen bonds : angle 4.85308 / 3.39 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5102.95 seconds wall clock time: 87 minutes 54.29 seconds (5274.29 seconds total)