Starting phenix.real_space_refine on Fri Mar 6 14:16:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o00_0564/03_2026/6o00_0564.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o00_0564/03_2026/6o00_0564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o00_0564/03_2026/6o00_0564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o00_0564/03_2026/6o00_0564.map" model { file = "/net/cci-nas-00/data/ceres_data/6o00_0564/03_2026/6o00_0564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o00_0564/03_2026/6o00_0564.cif" } resolution = 4.18 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= 0.001 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: 5 Type Number sf(0) Gaussians S 102 5.16 5 C 10398 2.51 5 N 2532 2.21 5 O 2724 1.98 5 H 15714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31470 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Time building chain proxies: 5.15, per 1000 atoms: 0.16 Number of scatterers: 31470 At special positions: 0 Unit cell: (109.888, 103.36, 131.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 102 16.00 O 2724 8.00 N 2532 7.00 C 10398 6.00 H 15714 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 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: 2.62 Conformation dependent library (CDL) restraints added in 932.1 milliseconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 76.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 47 removed outlier: 3.744A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 3.788A pdb=" N LEU A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 4.209A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 287 removed outlier: 3.805A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 346 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.857A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.744A pdb=" N THR B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 146 removed outlier: 3.506A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 3.788A pdb=" N LEU B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.513A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 287 removed outlier: 3.805A pdb=" N ILE B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 346 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 384 through 395 removed outlier: 4.311A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 21 " --> pdb=" O ARG C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.745A pdb=" N THR C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 3.787A pdb=" N LEU C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 256 removed outlier: 3.735A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 287 removed outlier: 3.805A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 346 Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'D' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 21 " --> pdb=" O ARG D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 removed outlier: 3.745A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 3.788A pdb=" N LEU D 131 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 287 removed outlier: 3.806A pdb=" N ILE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 Processing helix chain 'D' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'E' and resid 16 through 21 removed outlier: 3.858A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 21 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 removed outlier: 3.744A pdb=" N THR E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 116 Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.789A pdb=" N LEU E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.514A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 4.209A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 256 removed outlier: 3.736A pdb=" N LYS E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 287 removed outlier: 3.806A pdb=" N ILE E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 346 Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 Processing helix chain 'E' and resid 384 through 395 removed outlier: 4.313A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 394 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 408 Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.857A pdb=" N ILE F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 21 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 47 removed outlier: 3.745A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 116 Processing helix chain 'F' and resid 119 through 146 removed outlier: 3.507A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 3.788A pdb=" N LEU F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 140 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 166 removed outlier: 4.513A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 removed outlier: 4.208A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 256 removed outlier: 3.735A pdb=" N LYS F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 255 " --> pdb=" O ARG F 251 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 287 removed outlier: 3.806A pdb=" N ILE F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 346 Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.853A pdb=" N GLU F 358 " --> pdb=" O GLU F 354 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 384 through 395 removed outlier: 4.312A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 394 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AB1, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 61 984 hydrogen bonds defined for protein. 2898 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: 6.83 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 0.99: 15687 0.99 - 1.20: 12 1.20 - 1.40: 6939 1.40 - 1.61: 9138 1.61 - 1.81: 144 Bond restraints: 31920 Sorted by residual: bond pdb=" ND2 ASN A 408 " pdb="HD22 ASN A 408 " ideal model delta sigma weight residual 0.860 0.788 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" ND2 ASN D 408 " pdb="HD22 ASN D 408 " ideal model delta sigma weight residual 0.860 0.788 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CB ASN E 408 " pdb=" CG ASN E 408 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.68e+00 bond pdb=" CB ASN C 408 " pdb=" CG ASN C 408 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.63e+00 bond pdb=" CB ASN A 408 " pdb=" CG ASN A 408 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.62e+00 ... (remaining 31915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 57437 4.41 - 8.82: 120 8.82 - 13.23: 5 13.23 - 17.64: 0 17.64 - 22.04: 2 Bond angle restraints: 57564 Sorted by residual: angle pdb=" CG ASN F 408 " pdb=" ND2 ASN F 408 " pdb="HD21 ASN F 408 " ideal model delta sigma weight residual 120.00 97.96 22.04 3.00e+00 1.11e-01 5.40e+01 angle pdb=" CG ASN F 408 " pdb=" ND2 ASN F 408 " pdb="HD22 ASN F 408 " ideal model delta sigma weight residual 120.00 138.30 -18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" CG ASN D 408 " pdb=" ND2 ASN D 408 " pdb="HD21 ASN D 408 " ideal model delta sigma weight residual 120.00 131.91 -11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CG ASN A 408 " pdb=" ND2 ASN A 408 " pdb="HD21 ASN A 408 " ideal model delta sigma weight residual 120.00 131.86 -11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CG GLU E 236 " pdb=" CB GLU E 236 " pdb=" HB2 GLU E 236 " ideal model delta sigma weight residual 108.00 96.73 11.27 3.00e+00 1.11e-01 1.41e+01 ... (remaining 57559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 13097 16.11 - 32.23: 1470 32.23 - 48.34: 381 48.34 - 64.45: 142 64.45 - 80.56: 12 Dihedral angle restraints: 15102 sinusoidal: 7830 harmonic: 7272 Sorted by residual: dihedral pdb=" CA CYS F 139 " pdb=" C CYS F 139 " pdb=" N SER F 140 " pdb=" CA SER F 140 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS E 139 " pdb=" C CYS E 139 " pdb=" N SER E 140 " pdb=" CA SER E 140 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA CYS C 139 " pdb=" C CYS C 139 " pdb=" N SER C 140 " pdb=" CA SER C 140 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 15099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1416 0.028 - 0.055: 660 0.055 - 0.083: 229 0.083 - 0.110: 73 0.110 - 0.138: 28 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA VAL D 368 " pdb=" N VAL D 368 " pdb=" C VAL D 368 " pdb=" CB VAL D 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA VAL B 368 " pdb=" N VAL B 368 " pdb=" C VAL B 368 " pdb=" CB VAL B 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL A 368 " pdb=" N VAL A 368 " pdb=" C VAL A 368 " pdb=" CB VAL A 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 2403 not shown) Planarity restraints: 4458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 408 " 0.000 2.00e-02 2.50e+03 3.08e-02 1.42e+01 pdb=" CG ASN F 408 " 0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN F 408 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN F 408 " 0.061 2.00e-02 2.50e+03 pdb="HD21 ASN F 408 " -0.007 2.00e-02 2.50e+03 pdb="HD22 ASN F 408 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 408 " 0.023 2.00e-02 2.50e+03 2.39e-02 8.57e+00 pdb=" CG ASN D 408 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 408 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN D 408 " -0.031 2.00e-02 2.50e+03 pdb="HD21 ASN D 408 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN D 408 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 408 " 0.023 2.00e-02 2.50e+03 2.38e-02 8.52e+00 pdb=" CG ASN A 408 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 408 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 408 " -0.031 2.00e-02 2.50e+03 pdb="HD21 ASN A 408 " 0.039 2.00e-02 2.50e+03 pdb="HD22 ASN A 408 " -0.012 2.00e-02 2.50e+03 ... (remaining 4455 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 4775 2.27 - 2.85: 71485 2.85 - 3.44: 82478 3.44 - 4.02: 110366 4.02 - 4.60: 165791 Nonbonded interactions: 434895 Sorted by model distance: nonbonded pdb="HE21 GLN E 46 " pdb=" OD2 ASP E 50 " model vdw 1.688 2.450 nonbonded pdb="HE21 GLN F 46 " pdb=" OD2 ASP F 50 " model vdw 1.689 2.450 nonbonded pdb="HE21 GLN D 46 " pdb=" OD2 ASP D 50 " model vdw 1.689 2.450 nonbonded pdb="HE21 GLN B 46 " pdb=" OD2 ASP B 50 " model vdw 1.689 2.450 nonbonded pdb="HE21 GLN A 46 " pdb=" OD2 ASP A 50 " model vdw 1.689 2.450 ... (remaining 434890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 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: 0.200 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 27.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.005 0.041 16224 Z= 0.215 Angle : 0.724 6.250 21978 Z= 0.414 Chirality : 0.038 0.138 2406 Planarity : 0.004 0.051 2652 Dihedral : 14.218 80.564 5844 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.69 % Allowed : 2.06 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.18), residues: 1842 helix: -2.33 (0.12), residues: 1188 sheet: -2.52 (0.36), residues: 96 loop : -1.28 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 103 TYR 0.018 0.002 TYR F 106 PHE 0.014 0.002 PHE B 142 TRP 0.010 0.002 TRP B 143 HIS 0.007 0.002 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00459 (16206) covalent geometry : angle 0.72419 (21942) SS BOND : bond 0.00169 ( 18) SS BOND : angle 0.62191 ( 36) hydrogen bonds : bond 0.28380 ( 984) hydrogen bonds : angle 8.98771 ( 2898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 327 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 HIS cc_start: 0.8667 (t70) cc_final: 0.8411 (t-90) REVERT: A 265 MET cc_start: 0.8901 (tpt) cc_final: 0.8576 (tpt) REVERT: A 404 GLN cc_start: 0.8789 (mt0) cc_final: 0.8310 (tm-30) REVERT: B 404 GLN cc_start: 0.8764 (mt0) cc_final: 0.8154 (tm-30) REVERT: C 37 MET cc_start: 0.8853 (mtp) cc_final: 0.8559 (tmm) REVERT: C 164 PHE cc_start: 0.8575 (t80) cc_final: 0.8370 (t80) REVERT: C 236 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: D 165 ASP cc_start: 0.9267 (OUTLIER) cc_final: 0.8826 (p0) REVERT: D 236 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: E 236 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7902 (tp30) REVERT: E 253 HIS cc_start: 0.8686 (t70) cc_final: 0.8418 (t-90) REVERT: F 253 HIS cc_start: 0.8611 (t70) cc_final: 0.8397 (t-90) REVERT: F 265 MET cc_start: 0.8883 (tpt) cc_final: 0.8406 (tpt) REVERT: F 404 GLN cc_start: 0.8757 (mt0) cc_final: 0.8219 (tm-30) outliers start: 12 outliers final: 7 residues processed: 333 average time/residue: 0.3194 time to fit residues: 153.5506 Evaluate side-chains 213 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.065808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.055696 restraints weight = 255026.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.057874 restraints weight = 108926.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059012 restraints weight = 61369.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.059726 restraints weight = 43164.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060188 restraints weight = 33834.225| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16224 Z= 0.248 Angle : 0.648 5.662 21978 Z= 0.374 Chirality : 0.038 0.129 2406 Planarity : 0.005 0.039 2652 Dihedral : 5.014 22.299 2082 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -1.24 (0.18), residues: 1842 helix: -0.38 (0.13), residues: 1260 sheet: -2.15 (0.38), residues: 96 loop : -1.33 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 251 TYR 0.019 0.002 TYR A 17 PHE 0.018 0.002 PHE A 156 TRP 0.016 0.002 TRP A 168 HIS 0.014 0.002 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00498 (16206) covalent geometry : angle 0.64548 (21942) SS BOND : bond 0.00331 ( 18) SS BOND : angle 1.53177 ( 36) hydrogen bonds : bond 0.05991 ( 984) hydrogen bonds : angle 5.25888 ( 2898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8949 (m-30) cc_final: 0.8566 (p0) REVERT: A 253 HIS cc_start: 0.8993 (t70) cc_final: 0.8668 (t70) REVERT: A 265 MET cc_start: 0.8755 (tpt) cc_final: 0.8439 (tpp) REVERT: A 343 MET cc_start: 0.9041 (ttm) cc_final: 0.8264 (ttm) REVERT: A 404 GLN cc_start: 0.8734 (mt0) cc_final: 0.8062 (tm-30) REVERT: B 241 LYS cc_start: 0.9303 (ptmt) cc_final: 0.8965 (ttmt) REVERT: B 265 MET cc_start: 0.8634 (tpt) cc_final: 0.8071 (tpt) REVERT: B 404 GLN cc_start: 0.8758 (mt0) cc_final: 0.8036 (tm-30) REVERT: C 241 LYS cc_start: 0.9258 (ptmt) cc_final: 0.8817 (ttmt) REVERT: C 265 MET cc_start: 0.8649 (tpt) cc_final: 0.8179 (tpt) REVERT: C 404 GLN cc_start: 0.8823 (mt0) cc_final: 0.8116 (tm-30) REVERT: D 239 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8750 (mm-40) REVERT: E 265 MET cc_start: 0.8820 (tpt) cc_final: 0.8084 (tpt) REVERT: F 165 ASP cc_start: 0.8816 (m-30) cc_final: 0.8492 (p0) REVERT: F 404 GLN cc_start: 0.8792 (mt0) cc_final: 0.8113 (tm-30) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.2496 time to fit residues: 98.4331 Evaluate side-chains 190 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 105 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.065629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055584 restraints weight = 267042.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.057978 restraints weight = 110675.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.059369 restraints weight = 59340.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.060243 restraints weight = 38540.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.060715 restraints weight = 28717.910| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16224 Z= 0.187 Angle : 0.548 4.723 21978 Z= 0.317 Chirality : 0.035 0.132 2406 Planarity : 0.004 0.038 2652 Dihedral : 4.659 17.766 2082 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -0.25 (0.19), residues: 1842 helix: 0.54 (0.14), residues: 1284 sheet: -2.19 (0.37), residues: 96 loop : -1.47 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 251 TYR 0.014 0.002 TYR B 264 PHE 0.013 0.002 PHE E 156 TRP 0.014 0.001 TRP B 168 HIS 0.009 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00373 (16206) covalent geometry : angle 0.54684 (21942) SS BOND : bond 0.00406 ( 18) SS BOND : angle 1.02544 ( 36) hydrogen bonds : bond 0.05489 ( 984) hydrogen bonds : angle 4.73133 ( 2898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.9028 (m-30) cc_final: 0.8685 (p0) REVERT: A 265 MET cc_start: 0.8651 (tpt) cc_final: 0.8357 (tpt) REVERT: A 404 GLN cc_start: 0.8734 (mt0) cc_final: 0.8111 (tm-30) REVERT: B 265 MET cc_start: 0.8760 (tpt) cc_final: 0.8537 (tpp) REVERT: B 404 GLN cc_start: 0.8730 (mt0) cc_final: 0.7990 (tm-30) REVERT: C 239 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8917 (mm-40) REVERT: C 343 MET cc_start: 0.9003 (ttm) cc_final: 0.8468 (ttm) REVERT: D 253 HIS cc_start: 0.9096 (t70) cc_final: 0.8894 (t70) REVERT: D 337 MET cc_start: 0.9163 (tmm) cc_final: 0.8924 (tmm) REVERT: E 253 HIS cc_start: 0.9024 (t70) cc_final: 0.8807 (t70) REVERT: E 375 MET cc_start: 0.8909 (ptm) cc_final: 0.8683 (ptp) REVERT: F 165 ASP cc_start: 0.8798 (m-30) cc_final: 0.8466 (p0) REVERT: F 265 MET cc_start: 0.8503 (tpp) cc_final: 0.8288 (tpt) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2820 time to fit residues: 101.2457 Evaluate side-chains 183 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.065164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.054905 restraints weight = 251957.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.057083 restraints weight = 111974.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058280 restraints weight = 64868.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.059049 restraints weight = 44931.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.059493 restraints weight = 35156.318| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16224 Z= 0.221 Angle : 0.557 4.296 21978 Z= 0.322 Chirality : 0.035 0.134 2406 Planarity : 0.004 0.031 2652 Dihedral : 4.663 18.059 2082 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.09 (0.19), residues: 1842 helix: 0.81 (0.14), residues: 1284 sheet: -2.01 (0.35), residues: 96 loop : -1.43 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 251 TYR 0.016 0.002 TYR E 332 PHE 0.013 0.002 PHE F 324 TRP 0.018 0.002 TRP A 168 HIS 0.008 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00445 (16206) covalent geometry : angle 0.55630 (21942) SS BOND : bond 0.00390 ( 18) SS BOND : angle 1.02847 ( 36) hydrogen bonds : bond 0.04978 ( 984) hydrogen bonds : angle 4.58754 ( 2898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 MET cc_start: 0.8638 (tpt) cc_final: 0.8372 (tpt) REVERT: B 236 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8645 (mp0) REVERT: B 404 GLN cc_start: 0.8769 (mt0) cc_final: 0.8077 (tm-30) REVERT: C 239 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8790 (mm-40) REVERT: C 265 MET cc_start: 0.8542 (tpp) cc_final: 0.8336 (tpp) REVERT: C 343 MET cc_start: 0.9085 (ttm) cc_final: 0.8344 (ttm) REVERT: C 396 GLU cc_start: 0.9481 (pt0) cc_final: 0.9251 (pp20) REVERT: D 239 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8628 (mm-40) REVERT: D 253 HIS cc_start: 0.9101 (t70) cc_final: 0.8890 (t70) REVERT: D 337 MET cc_start: 0.9180 (tmm) cc_final: 0.8911 (tmm) REVERT: D 404 GLN cc_start: 0.8703 (mt0) cc_final: 0.7802 (tm-30) REVERT: F 343 MET cc_start: 0.9064 (ttm) cc_final: 0.8158 (ttm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2981 time to fit residues: 97.3771 Evaluate side-chains 172 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.065454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055794 restraints weight = 263598.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058034 restraints weight = 114034.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.059255 restraints weight = 63261.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.060046 restraints weight = 42861.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.060470 restraints weight = 32737.387| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16224 Z= 0.178 Angle : 0.517 4.117 21978 Z= 0.299 Chirality : 0.035 0.154 2406 Planarity : 0.004 0.030 2652 Dihedral : 4.533 16.920 2082 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 0.48 (0.19), residues: 1842 helix: 1.10 (0.14), residues: 1284 sheet: -1.50 (0.36), residues: 96 loop : -1.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.017 0.001 TYR D 351 PHE 0.012 0.001 PHE F 324 TRP 0.014 0.001 TRP A 168 HIS 0.006 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00355 (16206) covalent geometry : angle 0.51566 (21942) SS BOND : bond 0.00307 ( 18) SS BOND : angle 1.06493 ( 36) hydrogen bonds : bond 0.04736 ( 984) hydrogen bonds : angle 4.45054 ( 2898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.9046 (tmm) cc_final: 0.8826 (tmm) REVERT: B 236 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8743 (mp0) REVERT: B 265 MET cc_start: 0.8534 (tpp) cc_final: 0.8300 (tpp) REVERT: B 404 GLN cc_start: 0.8785 (mt0) cc_final: 0.8063 (tm-30) REVERT: C 239 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8674 (mm-40) REVERT: C 343 MET cc_start: 0.9150 (ttm) cc_final: 0.8455 (ttm) REVERT: D 253 HIS cc_start: 0.9133 (t70) cc_final: 0.8915 (t70) REVERT: D 337 MET cc_start: 0.9240 (tmm) cc_final: 0.8968 (tmm) REVERT: F 343 MET cc_start: 0.9149 (ttm) cc_final: 0.8692 (ttm) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2954 time to fit residues: 97.3301 Evaluate side-chains 172 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 62 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 111 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.063402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.053713 restraints weight = 265440.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055744 restraints weight = 117558.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.056897 restraints weight = 67731.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.057611 restraints weight = 46725.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.057999 restraints weight = 36256.607| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16224 Z= 0.256 Angle : 0.596 5.504 21978 Z= 0.345 Chirality : 0.037 0.167 2406 Planarity : 0.004 0.065 2652 Dihedral : 4.738 18.358 2082 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 1842 helix: 0.87 (0.14), residues: 1296 sheet: -1.62 (0.35), residues: 102 loop : -1.54 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 251 TYR 0.022 0.002 TYR F 351 PHE 0.014 0.002 PHE F 324 TRP 0.021 0.002 TRP A 168 HIS 0.009 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00510 (16206) covalent geometry : angle 0.59422 (21942) SS BOND : bond 0.00781 ( 18) SS BOND : angle 1.19104 ( 36) hydrogen bonds : bond 0.04876 ( 984) hydrogen bonds : angle 4.70817 ( 2898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.9044 (tmm) cc_final: 0.8818 (tmm) REVERT: B 404 GLN cc_start: 0.8825 (mt0) cc_final: 0.8089 (tm-30) REVERT: C 239 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8553 (mm-40) REVERT: C 337 MET cc_start: 0.9008 (tmm) cc_final: 0.8751 (tmm) REVERT: D 239 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8711 (mm-40) REVERT: F 164 PHE cc_start: 0.8675 (t80) cc_final: 0.8463 (t80) REVERT: F 343 MET cc_start: 0.9164 (ttm) cc_final: 0.8827 (ttm) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2855 time to fit residues: 86.0110 Evaluate side-chains 162 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.065739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.056213 restraints weight = 262550.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.058528 restraints weight = 110357.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.059943 restraints weight = 59301.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.060769 restraints weight = 38287.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.061325 restraints weight = 28739.197| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16224 Z= 0.120 Angle : 0.482 5.647 21978 Z= 0.276 Chirality : 0.035 0.152 2406 Planarity : 0.004 0.064 2652 Dihedral : 4.416 15.340 2082 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.20), residues: 1842 helix: 1.33 (0.14), residues: 1284 sheet: -0.85 (0.41), residues: 96 loop : -1.28 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 251 TYR 0.017 0.001 TYR E 308 PHE 0.010 0.001 PHE E 27 TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS F 155 Details of bonding type rmsd covalent geometry : bond 0.00245 (16206) covalent geometry : angle 0.48159 (21942) SS BOND : bond 0.00357 ( 18) SS BOND : angle 0.85357 ( 36) hydrogen bonds : bond 0.04380 ( 984) hydrogen bonds : angle 4.11621 ( 2898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8999 (m-30) cc_final: 0.8480 (p0) REVERT: A 265 MET cc_start: 0.8458 (tpp) cc_final: 0.8162 (tpt) REVERT: A 337 MET cc_start: 0.9038 (tmm) cc_final: 0.8824 (tmm) REVERT: A 343 MET cc_start: 0.8974 (ttm) cc_final: 0.8559 (ttm) REVERT: A 408 ASN cc_start: 0.7617 (t0) cc_final: 0.7366 (m110) REVERT: B 324 PHE cc_start: 0.8826 (t80) cc_final: 0.8625 (t80) REVERT: B 404 GLN cc_start: 0.8717 (mt0) cc_final: 0.8032 (tm-30) REVERT: C 239 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8466 (mm-40) REVERT: C 337 MET cc_start: 0.9006 (tmm) cc_final: 0.8745 (tmm) REVERT: D 239 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8706 (mm110) REVERT: D 337 MET cc_start: 0.9037 (tmm) cc_final: 0.8749 (tmm) REVERT: E 265 MET cc_start: 0.8440 (tpp) cc_final: 0.7929 (tpt) REVERT: F 164 PHE cc_start: 0.8543 (t80) cc_final: 0.8302 (t80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2827 time to fit residues: 95.9003 Evaluate side-chains 179 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 174 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.065350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.055650 restraints weight = 255549.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.057959 restraints weight = 110826.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.059347 restraints weight = 60453.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.060223 restraints weight = 39310.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.060846 restraints weight = 29451.105| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16224 Z= 0.135 Angle : 0.482 4.970 21978 Z= 0.277 Chirality : 0.034 0.132 2406 Planarity : 0.004 0.041 2652 Dihedral : 4.308 15.327 2082 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.96 (0.20), residues: 1842 helix: 1.44 (0.14), residues: 1290 sheet: -0.58 (0.41), residues: 96 loop : -1.37 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 251 TYR 0.013 0.001 TYR E 305 PHE 0.014 0.001 PHE A 164 TRP 0.013 0.001 TRP B 168 HIS 0.018 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00276 (16206) covalent geometry : angle 0.48183 (21942) SS BOND : bond 0.00238 ( 18) SS BOND : angle 0.75905 ( 36) hydrogen bonds : bond 0.04236 ( 984) hydrogen bonds : angle 4.05301 ( 2898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8973 (m-30) cc_final: 0.8366 (p0) REVERT: A 265 MET cc_start: 0.8416 (tpp) cc_final: 0.8167 (tpt) REVERT: A 337 MET cc_start: 0.8998 (tmm) cc_final: 0.8788 (tmm) REVERT: A 343 MET cc_start: 0.8990 (ttm) cc_final: 0.8442 (ttm) REVERT: B 241 LYS cc_start: 0.9054 (ptmt) cc_final: 0.8696 (ttpt) REVERT: B 404 GLN cc_start: 0.8703 (mt0) cc_final: 0.8043 (tm-30) REVERT: C 337 MET cc_start: 0.8998 (tmm) cc_final: 0.8721 (tmm) REVERT: C 343 MET cc_start: 0.9240 (ttt) cc_final: 0.9022 (ttt) REVERT: E 236 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8417 (mp0) REVERT: E 324 PHE cc_start: 0.8914 (t80) cc_final: 0.8652 (t80) REVERT: F 164 PHE cc_start: 0.8461 (t80) cc_final: 0.8217 (t80) REVERT: F 171 ARG cc_start: 0.9218 (ttm110) cc_final: 0.8319 (ttp80) REVERT: F 324 PHE cc_start: 0.8882 (t80) cc_final: 0.8609 (t80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2768 time to fit residues: 88.1900 Evaluate side-chains 173 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 184 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.066621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056878 restraints weight = 250901.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.059292 restraints weight = 106863.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.060650 restraints weight = 57573.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.061602 restraints weight = 37961.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.062187 restraints weight = 27729.845| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16224 Z= 0.105 Angle : 0.455 5.727 21978 Z= 0.258 Chirality : 0.034 0.133 2406 Planarity : 0.003 0.032 2652 Dihedral : 4.135 14.688 2082 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 1.23 (0.20), residues: 1842 helix: 1.61 (0.14), residues: 1290 sheet: -0.11 (0.41), residues: 96 loop : -1.26 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 251 TYR 0.013 0.001 TYR E 305 PHE 0.009 0.001 PHE D 250 TRP 0.009 0.001 TRP D 168 HIS 0.015 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00214 (16206) covalent geometry : angle 0.45420 (21942) SS BOND : bond 0.00208 ( 18) SS BOND : angle 0.64345 ( 36) hydrogen bonds : bond 0.03983 ( 984) hydrogen bonds : angle 3.83768 ( 2898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8973 (m-30) cc_final: 0.8325 (p0) REVERT: A 265 MET cc_start: 0.8327 (tpp) cc_final: 0.8038 (tpt) REVERT: A 343 MET cc_start: 0.9007 (ttm) cc_final: 0.8317 (ttm) REVERT: B 404 GLN cc_start: 0.8691 (mt0) cc_final: 0.8022 (tm-30) REVERT: C 324 PHE cc_start: 0.8796 (t80) cc_final: 0.8594 (t80) REVERT: C 337 MET cc_start: 0.8968 (tmm) cc_final: 0.8722 (tmm) REVERT: D 324 PHE cc_start: 0.8703 (t80) cc_final: 0.8392 (t80) REVERT: E 236 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8376 (mp0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2865 time to fit residues: 97.5359 Evaluate side-chains 181 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 45 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 134 optimal weight: 0.0050 chunk 120 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.067421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056361 restraints weight = 243380.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.058885 restraints weight = 106004.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.060348 restraints weight = 60170.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.061351 restraints weight = 40564.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062007 restraints weight = 30290.262| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16224 Z= 0.118 Angle : 0.466 5.869 21978 Z= 0.266 Chirality : 0.034 0.132 2406 Planarity : 0.004 0.033 2652 Dihedral : 4.095 14.780 2082 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.34 (0.20), residues: 1842 helix: 1.68 (0.14), residues: 1290 sheet: 0.07 (0.42), residues: 96 loop : -1.23 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 251 TYR 0.016 0.001 TYR D 325 PHE 0.021 0.001 PHE D 275 TRP 0.013 0.001 TRP C 168 HIS 0.015 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00239 (16206) covalent geometry : angle 0.46625 (21942) SS BOND : bond 0.00198 ( 18) SS BOND : angle 0.58728 ( 36) hydrogen bonds : bond 0.03934 ( 984) hydrogen bonds : angle 3.85104 ( 2898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASP cc_start: 0.8922 (m-30) cc_final: 0.8325 (p0) REVERT: A 265 MET cc_start: 0.8381 (tpp) cc_final: 0.8178 (tpt) REVERT: A 343 MET cc_start: 0.9035 (ttm) cc_final: 0.8422 (ttm) REVERT: B 404 GLN cc_start: 0.8747 (mt0) cc_final: 0.8063 (tm-30) REVERT: C 337 MET cc_start: 0.9073 (tmm) cc_final: 0.8837 (tmm) REVERT: D 27 PHE cc_start: 0.8226 (m-80) cc_final: 0.7944 (m-80) REVERT: D 265 MET cc_start: 0.8445 (tpp) cc_final: 0.8006 (tpt) REVERT: D 324 PHE cc_start: 0.8773 (t80) cc_final: 0.8485 (t80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.2861 time to fit residues: 92.7371 Evaluate side-chains 176 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 78 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.066732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.055772 restraints weight = 244580.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.058219 restraints weight = 107239.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.059636 restraints weight = 61579.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.060589 restraints weight = 41928.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.061143 restraints weight = 31593.685| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16224 Z= 0.162 Angle : 0.500 6.013 21978 Z= 0.287 Chirality : 0.034 0.140 2406 Planarity : 0.004 0.038 2652 Dihedral : 4.187 15.234 2082 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 1.23 (0.20), residues: 1842 helix: 1.60 (0.14), residues: 1296 sheet: -0.09 (0.40), residues: 102 loop : -1.27 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 251 TYR 0.015 0.001 TYR D 264 PHE 0.014 0.001 PHE B 318 TRP 0.016 0.002 TRP B 168 HIS 0.016 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00326 (16206) covalent geometry : angle 0.49980 (21942) SS BOND : bond 0.00245 ( 18) SS BOND : angle 0.63311 ( 36) hydrogen bonds : bond 0.04092 ( 984) hydrogen bonds : angle 4.01460 ( 2898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4251.63 seconds wall clock time: 73 minutes 49.15 seconds (4429.15 seconds total)