Starting phenix.real_space_refine on Sat Oct 24 15:47:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26fv_80619/10_2026/26fv_80619.cif Found real_map, /net/cci-nas-00/data/ceres_data/26fv_80619/10_2026/26fv_80619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/26fv_80619/10_2026/26fv_80619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26fv_80619/10_2026/26fv_80619.map" model { file = "/net/cci-nas-00/data/ceres_data/26fv_80619/10_2026/26fv_80619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26fv_80619/10_2026/26fv_80619.cif" } resolution = 3.34 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= 0.045 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 P 4 5.49 5 S 60 5.16 5 C 8492 2.51 5 N 2340 2.21 5 O 2652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13548 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "B" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "C" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "D" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3366 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IK2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IK2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IK2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'IK2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 0.23 Number of scatterers: 13548 At special positions: 0 Unit cell: (80.96, 146.28, 89.24, 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 60 16.00 P 4 15.00 O 2652 8.00 N 2340 7.00 C 8492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 629.1 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 21 sheets defined 41.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 4.046A pdb=" N ILE A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.544A pdb=" N ALA A 48 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 4.898A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.601A pdb=" N SER A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.642A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 195 through 198 removed outlier: 3.507A pdb=" N GLY A 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 198' Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.566A pdb=" N ASP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 3.764A pdb=" N MET A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.670A pdb=" N TYR A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.812A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 388 through 396 removed outlier: 4.395A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 removed outlier: 3.508A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'B' and resid 6 through 11 removed outlier: 4.018A pdb=" N ILE B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.520A pdb=" N LYS B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.606A pdb=" N VAL B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.614A pdb=" N SER B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.589A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 195 through 198 removed outlier: 3.542A pdb=" N GLY B 198 " --> pdb=" O GLU B 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 247 through 263 removed outlier: 3.566A pdb=" N ASP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 284 removed outlier: 3.607A pdb=" N GLY B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.660A pdb=" N TYR B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.033A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 388 through 396 removed outlier: 4.462A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'C' and resid 6 through 11 removed outlier: 4.038A pdb=" N ILE C 11 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.697A pdb=" N ALA C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 removed outlier: 4.264A pdb=" N GLY C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LEU C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.535A pdb=" N ARG C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.581A pdb=" N SER C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.501A pdb=" N ASN C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.526A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 184 through 194 removed outlier: 3.558A pdb=" N GLY C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.516A pdb=" N GLY C 198 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 247 through 263 removed outlier: 3.555A pdb=" N ASP C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 284 removed outlier: 3.554A pdb=" N GLY C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 284 " --> pdb=" O VAL C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.642A pdb=" N TYR C 314 " --> pdb=" O TRP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 removed outlier: 3.784A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 388 through 396 removed outlier: 4.446A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 430 removed outlier: 3.523A pdb=" N LEU C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 460 Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.112A pdb=" N ILE D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.865A pdb=" N ALA D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 87 removed outlier: 5.152A pdb=" N LEU D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.593A pdb=" N SER D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 161 removed outlier: 3.517A pdb=" N ALA D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 170 Processing helix chain 'D' and resid 184 through 194 removed outlier: 3.710A pdb=" N GLY D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 removed outlier: 3.557A pdb=" N GLY D 198 " --> pdb=" O GLU D 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 195 through 198' Processing helix chain 'D' and resid 247 through 263 removed outlier: 3.571A pdb=" N ASP D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 284 removed outlier: 4.836A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.650A pdb=" N TYR D 314 " --> pdb=" O TRP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 removed outlier: 3.982A pdb=" N VAL D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 388 through 396 removed outlier: 4.441A pdb=" N PHE D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 430 removed outlier: 3.515A pdb=" N LEU D 430 " --> pdb=" O ALA D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 6.166A pdb=" N ILE A 67 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 208 removed outlier: 5.849A pdb=" N GLY A 205 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL A 246 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP A 207 " --> pdb=" O VAL A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.530A pdb=" N VAL A 370 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY A 384 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 416 through 417 removed outlier: 6.647A pdb=" N LEU A 436 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL A 447 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 438 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.810A pdb=" N LEU B 294 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.091A pdb=" N ILE B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 205 through 208 removed outlier: 5.872A pdb=" N GLY B 205 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 246 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.642A pdb=" N VAL B 370 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY B 384 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 416 through 417 removed outlier: 6.548A pdb=" N ILE B 417 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 436 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B 447 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL B 438 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.671A pdb=" N LEU C 294 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 112 through 113 removed outlier: 6.209A pdb=" N ILE C 67 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP C 143 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 205 through 208 removed outlier: 5.863A pdb=" N GLY C 205 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL C 246 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP C 207 " --> pdb=" O VAL C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.638A pdb=" N VAL C 370 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 384 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 416 through 417 removed outlier: 6.546A pdb=" N ILE C 417 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU C 436 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL C 447 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 438 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.805A pdb=" N LEU D 294 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 113 removed outlier: 5.886A pdb=" N ILE D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR D 66 " --> pdb=" O TRP D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 205 through 208 removed outlier: 5.873A pdb=" N GLY D 205 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL D 246 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP D 207 " --> pdb=" O VAL D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 367 through 370 removed outlier: 3.708A pdb=" N VAL D 370 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 384 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 416 through 417 removed outlier: 6.706A pdb=" N LEU D 436 " --> pdb=" O VAL D 447 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL D 447 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL D 438 " --> pdb=" O VAL D 445 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2354 1.31 - 1.44: 3386 1.44 - 1.56: 7972 1.56 - 1.69: 4 1.69 - 1.81: 104 Bond restraints: 13820 Sorted by residual: bond pdb=" C THR D 185 " pdb=" O THR D 185 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.92e+01 bond pdb=" O4P IK2 C 501 " pdb=" P IK2 C 501 " ideal model delta sigma weight residual 1.682 1.596 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" O4P IK2 A 501 " pdb=" P IK2 A 501 " ideal model delta sigma weight residual 1.682 1.596 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" CA SER C 411 " pdb=" CB SER C 411 " ideal model delta sigma weight residual 1.530 1.462 0.067 1.58e-02 4.01e+03 1.82e+01 bond pdb=" O4P IK2 D 501 " pdb=" P IK2 D 501 " ideal model delta sigma weight residual 1.682 1.598 0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 13815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 18008 1.46 - 2.93: 558 2.93 - 4.39: 192 4.39 - 5.86: 31 5.86 - 7.32: 7 Bond angle restraints: 18796 Sorted by residual: angle pdb=" CA THR A 185 " pdb=" CB THR A 185 " pdb=" OG1 THR A 185 " ideal model delta sigma weight residual 109.60 102.30 7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" CA ASP C 332 " pdb=" CB ASP C 332 " pdb=" CG ASP C 332 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.00e+00 1.00e+00 2.29e+01 angle pdb=" N SER A 132 " pdb=" CA SER A 132 " pdb=" C SER A 132 " ideal model delta sigma weight residual 111.36 106.39 4.97 1.09e+00 8.42e-01 2.08e+01 angle pdb=" C LYS A 102 " pdb=" CA LYS A 102 " pdb=" CB LYS A 102 " ideal model delta sigma weight residual 110.88 103.80 7.08 1.57e+00 4.06e-01 2.03e+01 angle pdb=" CA GLN C 84 " pdb=" C GLN C 84 " pdb=" O GLN C 84 " ideal model delta sigma weight residual 120.42 115.69 4.73 1.06e+00 8.90e-01 1.99e+01 ... (remaining 18791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 7689 16.01 - 32.02: 431 32.02 - 48.03: 97 48.03 - 64.03: 33 64.03 - 80.04: 10 Dihedral angle restraints: 8260 sinusoidal: 3164 harmonic: 5096 Sorted by residual: dihedral pdb=" N THR C 182 " pdb=" C THR C 182 " pdb=" CA THR C 182 " pdb=" CB THR C 182 " ideal model delta harmonic sigma weight residual 123.40 113.96 9.44 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" CA TYR C 314 " pdb=" C TYR C 314 " pdb=" N GLY C 315 " pdb=" CA GLY C 315 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA TYR D 314 " pdb=" C TYR D 314 " pdb=" N GLY D 315 " pdb=" CA GLY D 315 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1499 0.040 - 0.079: 387 0.079 - 0.119: 198 0.119 - 0.158: 18 0.158 - 0.198: 2 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA GLU A 100 " pdb=" N GLU A 100 " pdb=" C GLU A 100 " pdb=" CB GLU A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA ILE D 417 " pdb=" N ILE D 417 " pdb=" C ILE D 417 " pdb=" CB ILE D 417 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA MET D 416 " pdb=" N MET D 416 " pdb=" C MET D 416 " pdb=" CB MET D 416 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2101 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 185 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR B 185 " -0.059 2.00e-02 2.50e+03 pdb=" O THR B 185 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE B 186 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 185 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.94e+00 pdb=" C THR D 185 " 0.052 2.00e-02 2.50e+03 pdb=" O THR D 185 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE D 186 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 411 " -0.013 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C SER C 411 " 0.042 2.00e-02 2.50e+03 pdb=" O SER C 411 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO C 412 " -0.014 2.00e-02 2.50e+03 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1696 2.74 - 3.28: 14656 3.28 - 3.82: 21115 3.82 - 4.36: 25683 4.36 - 4.90: 41365 Nonbonded interactions: 104515 Sorted by model distance: nonbonded pdb=" OD1 ASN A 150 " pdb=" N GLY A 153 " model vdw 2.206 3.120 nonbonded pdb=" O PRO A 208 " pdb=" OG SER A 211 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN D 150 " pdb=" N GLY D 153 " model vdw 2.210 3.120 nonbonded pdb=" O PRO D 208 " pdb=" OG SER D 211 " model vdw 2.211 3.040 nonbonded pdb=" O PRO C 208 " pdb=" OG SER C 211 " model vdw 2.220 3.040 ... (remaining 104510 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.930 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4812 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13820 Z= 0.261 Angle : 0.682 7.321 18796 Z= 0.416 Chirality : 0.044 0.198 2104 Planarity : 0.004 0.036 2476 Dihedral : 11.496 80.043 5052 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.44 % Favored : 91.45 % Rotamer: Outliers : 6.70 % Allowed : 9.90 % Favored : 83.40 % 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: -2.36 (0.19), residues: 1824 helix: -0.78 (0.22), residues: 600 sheet: -1.92 (0.39), residues: 212 loop : -2.00 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 361 TYR 0.009 0.001 TYR B 36 PHE 0.009 0.001 PHE B 316 TRP 0.004 0.001 TRP A 166 HIS 0.007 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.26 (13820) covalent geometry : angle 0.68232 / 0.42 (18796) hydrogen bonds : bond 0.28232 / 19.72 ( 447) hydrogen bonds : angle 9.57918 / 6.78 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 335 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.4693 (tpp80) cc_final: 0.4337 (mtp180) REVERT: A 52 ILE cc_start: 0.5361 (mm) cc_final: 0.4905 (tp) REVERT: A 86 ARG cc_start: 0.7094 (tpp80) cc_final: 0.6116 (mtm110) REVERT: A 302 MET cc_start: 0.4937 (mmm) cc_final: 0.3553 (mmp) REVERT: A 311 MET cc_start: 0.5660 (ttm) cc_final: 0.5417 (ttt) REVERT: A 316 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6606 (p90) REVERT: A 378 MET cc_start: 0.4270 (tpt) cc_final: 0.3489 (ptm) REVERT: A 410 MET cc_start: 0.5034 (ppp) cc_final: 0.4433 (ptp) REVERT: A 416 MET cc_start: 0.2152 (mtm) cc_final: 0.1919 (mmm) REVERT: B 37 LEU cc_start: 0.6113 (mt) cc_final: 0.5574 (tt) REVERT: B 69 GLU cc_start: 0.6666 (pp20) cc_final: 0.6312 (pp20) REVERT: B 71 THR cc_start: 0.8295 (t) cc_final: 0.7661 (t) REVERT: B 86 ARG cc_start: 0.7087 (tpp80) cc_final: 0.6189 (mtm180) REVERT: B 180 ILE cc_start: 0.5751 (tt) cc_final: 0.5043 (tt) REVERT: B 185 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6399 (m) REVERT: B 201 VAL cc_start: 0.5658 (p) cc_final: 0.5396 (p) REVERT: B 235 TYR cc_start: 0.4721 (t80) cc_final: 0.4353 (t80) REVERT: B 302 MET cc_start: 0.4877 (mmm) cc_final: 0.3552 (mmp) REVERT: B 311 MET cc_start: 0.5716 (ttm) cc_final: 0.5473 (ttt) REVERT: B 316 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6665 (p90) REVERT: B 378 MET cc_start: 0.4110 (tpt) cc_final: 0.3728 (tpt) REVERT: B 437 MET cc_start: 0.2150 (ttp) cc_final: 0.1716 (ttp) REVERT: C 46 ARG cc_start: 0.3761 (ttm110) cc_final: 0.3521 (ttm-80) REVERT: C 86 ARG cc_start: 0.7083 (tpp80) cc_final: 0.6030 (mtm110) REVERT: C 235 TYR cc_start: 0.4576 (t80) cc_final: 0.4278 (t80) REVERT: C 279 LYS cc_start: 0.6676 (tttt) cc_final: 0.6216 (ptmt) REVERT: C 302 MET cc_start: 0.4860 (mmm) cc_final: 0.3393 (mmp) REVERT: C 311 MET cc_start: 0.5667 (ttm) cc_final: 0.5432 (ttt) REVERT: C 316 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6525 (p90) REVERT: C 347 THR cc_start: 0.7359 (m) cc_final: 0.6949 (p) REVERT: C 378 MET cc_start: 0.4558 (tpt) cc_final: 0.3684 (ptm) REVERT: C 414 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.4608 (pt) REVERT: D 46 ARG cc_start: 0.4067 (ttm110) cc_final: 0.3681 (ttm-80) REVERT: D 71 THR cc_start: 0.7758 (t) cc_final: 0.7250 (t) REVERT: D 86 ARG cc_start: 0.7082 (tpp80) cc_final: 0.5987 (mtm110) REVERT: D 235 TYR cc_start: 0.4613 (t80) cc_final: 0.4285 (t80) REVERT: D 279 LYS cc_start: 0.6679 (tttt) cc_final: 0.6215 (ptmt) REVERT: D 302 MET cc_start: 0.4913 (mmm) cc_final: 0.3929 (mmp) REVERT: D 311 MET cc_start: 0.5700 (ttm) cc_final: 0.5452 (ttt) REVERT: D 316 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6639 (p90) REVERT: D 347 THR cc_start: 0.7336 (m) cc_final: 0.6853 (p) REVERT: D 378 MET cc_start: 0.4294 (tpt) cc_final: 0.3553 (ptm) REVERT: D 401 LYS cc_start: 0.6593 (mtmt) cc_final: 0.6388 (mptt) REVERT: D 436 LEU cc_start: 0.5624 (pp) cc_final: 0.5391 (mt) outliers start: 94 outliers final: 24 residues processed: 408 average time/residue: 0.1219 time to fit residues: 70.8418 Evaluate side-chains 267 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.282959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.271118 restraints weight = 14993.798| |-----------------------------------------------------------------------------| r_work (start): 0.4764 rms_B_bonded: 1.70 r_work: 0.4693 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4576 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13820 Z= 0.131 Angle : 0.631 7.684 18796 Z= 0.319 Chirality : 0.045 0.152 2104 Planarity : 0.005 0.041 2476 Dihedral : 7.982 106.218 2092 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 4.84 % Allowed : 17.95 % Favored : 77.21 % 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: -1.95 (0.19), residues: 1824 helix: -0.61 (0.19), residues: 672 sheet: -2.11 (0.39), residues: 196 loop : -1.58 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 18 TYR 0.014 0.002 TYR B 192 PHE 0.012 0.001 PHE A 316 TRP 0.008 0.002 TRP D 166 HIS 0.007 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13820) covalent geometry : angle 0.63065 / 0.32 (18796) hydrogen bonds : bond 0.04679 / 3.27 ( 447) hydrogen bonds : angle 5.64893 / 3.98 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6704 (tm-30) REVERT: A 71 THR cc_start: 0.7770 (t) cc_final: 0.7514 (t) REVERT: A 94 CYS cc_start: 0.7046 (m) cc_final: 0.6792 (m) REVERT: B 37 LEU cc_start: 0.6497 (mt) cc_final: 0.6185 (tt) REVERT: B 180 ILE cc_start: 0.6771 (tt) cc_final: 0.6401 (tt) REVERT: B 436 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5531 (pp) REVERT: C 37 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6804 (mm) REVERT: C 46 ARG cc_start: 0.5322 (ttm110) cc_final: 0.5038 (ttp-170) REVERT: C 53 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6625 (tm-30) REVERT: C 219 ARG cc_start: 0.6122 (ttp-170) cc_final: 0.5879 (ttp-170) REVERT: C 260 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6328 (mtt-85) REVERT: C 414 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6263 (pt) REVERT: D 53 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6703 (tm-30) REVERT: D 219 ARG cc_start: 0.6106 (ttp-170) cc_final: 0.5895 (ttp-170) REVERT: D 437 MET cc_start: 0.4849 (ttp) cc_final: 0.4595 (mtm) outliers start: 68 outliers final: 37 residues processed: 308 average time/residue: 0.1180 time to fit residues: 52.1709 Evaluate side-chains 259 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 443 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [23, 86, 43, 149, 164, 151, 21, 24, 19, 165, 143] chunk 23 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 0.0670 chunk 143 optimal weight: 6.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN B 367 GLN C 367 GLN D 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5091 r_free = 0.5091 target = 0.300088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.286489 restraints weight = 16226.689| |-----------------------------------------------------------------------------| r_work (start): 0.4952 rms_B_bonded: 1.99 r_work: 0.4855 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13820 Z= 0.120 Angle : 0.603 8.926 18796 Z= 0.302 Chirality : 0.044 0.163 2104 Planarity : 0.005 0.041 2476 Dihedral : 7.655 104.133 2069 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 5.70 % Allowed : 18.87 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.19), residues: 1824 helix: -0.46 (0.19), residues: 680 sheet: -1.78 (0.38), residues: 196 loop : -1.45 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.013 0.002 TYR B 192 PHE 0.011 0.001 PHE A 316 TRP 0.008 0.001 TRP B 231 HIS 0.004 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13820) covalent geometry : angle 0.60255 / 0.30 (18796) hydrogen bonds : bond 0.03527 / 2.45 ( 447) hydrogen bonds : angle 5.31727 / 3.73 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.6177 (ttp-170) cc_final: 0.5621 (ttp-170) REVERT: A 242 GLU cc_start: 0.6372 (pp20) cc_final: 0.6165 (pt0) REVERT: A 416 MET cc_start: 0.2520 (ptp) cc_final: 0.2209 (ptt) REVERT: A 441 GLU cc_start: 0.7149 (mp0) cc_final: 0.6932 (mp0) REVERT: B 37 LEU cc_start: 0.6687 (mt) cc_final: 0.6377 (tt) REVERT: B 242 GLU cc_start: 0.6716 (pp20) cc_final: 0.6332 (pt0) REVERT: B 410 MET cc_start: 0.5899 (ptp) cc_final: 0.5573 (mtm) REVERT: B 441 GLU cc_start: 0.7195 (mp0) cc_final: 0.6943 (mp0) REVERT: C 219 ARG cc_start: 0.6031 (ttp-170) cc_final: 0.5686 (ttp-170) REVERT: C 242 GLU cc_start: 0.6715 (pp20) cc_final: 0.6258 (pt0) REVERT: C 260 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6528 (mtt-85) REVERT: C 279 LYS cc_start: 0.6911 (tmtt) cc_final: 0.6252 (ttmm) REVERT: D 219 ARG cc_start: 0.6017 (ttp-170) cc_final: 0.5629 (ttp-170) REVERT: D 279 LYS cc_start: 0.6849 (tmtt) cc_final: 0.6221 (ttmm) REVERT: D 378 MET cc_start: 0.6256 (ptm) cc_final: 0.6055 (ptp) REVERT: D 410 MET cc_start: 0.6226 (ptp) cc_final: 0.5885 (mtm) outliers start: 80 outliers final: 44 residues processed: 295 average time/residue: 0.1265 time to fit residues: 52.7396 Evaluate side-chains 260 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 443 LYS Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 437 MET Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 443 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [83, 131, 4, 69, 110, 32, 53, 149, 68, 117, 108] chunk 83 optimal weight: 0.0970 chunk 131 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.292586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.278835 restraints weight = 16185.706| |-----------------------------------------------------------------------------| r_work (start): 0.4904 rms_B_bonded: 1.92 r_work: 0.4802 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.4802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13820 Z= 0.184 Angle : 0.688 7.623 18796 Z= 0.350 Chirality : 0.048 0.155 2104 Planarity : 0.006 0.059 2476 Dihedral : 8.153 94.734 2062 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.44 % Favored : 91.50 % Rotamer: Outliers : 6.98 % Allowed : 18.09 % Favored : 74.93 % 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: -2.17 (0.18), residues: 1824 helix: -0.79 (0.18), residues: 696 sheet: -1.93 (0.28), residues: 292 loop : -1.72 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 354 TYR 0.018 0.002 TYR B 192 PHE 0.015 0.002 PHE A 316 TRP 0.016 0.002 TRP D 231 HIS 0.007 0.002 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (13820) covalent geometry : angle 0.68847 / 0.35 (18796) hydrogen bonds : bond 0.03755 / 2.63 ( 447) hydrogen bonds : angle 5.48442 / 3.86 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 259 time to evaluate : 0.451 Fit side-chains REVERT: A 35 GLU cc_start: 0.5930 (mm-30) cc_final: 0.5695 (mm-30) REVERT: A 180 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6782 (tp) REVERT: A 193 LEU cc_start: 0.7208 (mm) cc_final: 0.6956 (mm) REVERT: A 219 ARG cc_start: 0.6662 (ttp-170) cc_final: 0.5498 (ttp-170) REVERT: A 441 GLU cc_start: 0.7202 (mp0) cc_final: 0.6960 (mp0) REVERT: A 448 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5825 (tt) REVERT: B 5 GLN cc_start: 0.6531 (tp40) cc_final: 0.6219 (mp10) REVERT: B 219 ARG cc_start: 0.6707 (ttp-170) cc_final: 0.5653 (ttp-170) REVERT: B 242 GLU cc_start: 0.6927 (pp20) cc_final: 0.6565 (pt0) REVERT: C 107 ILE cc_start: 0.7764 (pt) cc_final: 0.7447 (mt) REVERT: C 219 ARG cc_start: 0.6784 (ttp-170) cc_final: 0.5737 (ttp-170) REVERT: C 242 GLU cc_start: 0.6722 (pp20) cc_final: 0.6396 (pt0) REVERT: C 260 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7105 (mtt180) REVERT: C 279 LYS cc_start: 0.7103 (tmtt) cc_final: 0.6442 (ttmm) REVERT: C 436 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5990 (pp) REVERT: D 5 GLN cc_start: 0.6584 (tp40) cc_final: 0.6217 (pt0) REVERT: D 219 ARG cc_start: 0.6821 (ttp-170) cc_final: 0.5755 (ttp-170) REVERT: D 279 LYS cc_start: 0.7205 (tmtt) cc_final: 0.6525 (ttmm) REVERT: D 378 MET cc_start: 0.6838 (ptm) cc_final: 0.6519 (ptp) REVERT: D 441 GLU cc_start: 0.7084 (mp0) cc_final: 0.6721 (mp0) outliers start: 98 outliers final: 55 residues processed: 327 average time/residue: 0.1246 time to fit residues: 57.6854 Evaluate side-chains 277 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 218 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [151, 51, 59, 92, 162, 91, 26, 45, 49, 3, 165] chunk 151 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 49 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 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 = 0.5064 r_free = 0.5064 target = 0.298848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.284150 restraints weight = 16384.589| |-----------------------------------------------------------------------------| r_work (start): 0.4934 rms_B_bonded: 2.12 r_work: 0.4827 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13820 Z= 0.117 Angle : 0.589 6.802 18796 Z= 0.298 Chirality : 0.044 0.150 2104 Planarity : 0.005 0.044 2476 Dihedral : 7.676 102.153 2061 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.76 % Favored : 94.19 % Rotamer: Outliers : 5.27 % Allowed : 20.73 % Favored : 74.00 % 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: -1.77 (0.18), residues: 1824 helix: -0.43 (0.19), residues: 680 sheet: -1.56 (0.35), residues: 212 loop : -1.63 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.036 0.001 TYR A 314 PHE 0.016 0.002 PHE A 316 TRP 0.006 0.001 TRP C 231 HIS 0.003 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (13820) covalent geometry : angle 0.58864 / 0.30 (18796) hydrogen bonds : bond 0.03142 / 2.15 ( 447) hydrogen bonds : angle 5.28853 / 3.72 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 231 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6746 (pt0) cc_final: 0.6315 (mp10) REVERT: A 219 ARG cc_start: 0.6576 (ttp-170) cc_final: 0.5540 (ttp-170) REVERT: A 378 MET cc_start: 0.6408 (ptp) cc_final: 0.5864 (ppp) REVERT: A 441 GLU cc_start: 0.7218 (mp0) cc_final: 0.6975 (mp0) REVERT: B 5 GLN cc_start: 0.6199 (tp40) cc_final: 0.5815 (mp10) REVERT: B 242 GLU cc_start: 0.6810 (pp20) cc_final: 0.6413 (pt0) REVERT: C 5 GLN cc_start: 0.6605 (pt0) cc_final: 0.6218 (mp10) REVERT: C 219 ARG cc_start: 0.6695 (ttp-170) cc_final: 0.5718 (ttp-170) REVERT: C 242 GLU cc_start: 0.6709 (pp20) cc_final: 0.6412 (pt0) REVERT: C 260 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6729 (mtt-85) REVERT: C 279 LYS cc_start: 0.7092 (tmtt) cc_final: 0.6417 (ptpp) REVERT: D 219 ARG cc_start: 0.6756 (ttp-170) cc_final: 0.5754 (ttp-170) REVERT: D 279 LYS cc_start: 0.7193 (tmtt) cc_final: 0.6041 (ttmm) outliers start: 74 outliers final: 50 residues processed: 290 average time/residue: 0.1246 time to fit residues: 51.6092 Evaluate side-chains 267 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [151, 35, 153, 30, 79, 7, 129, 106, 5, 150, 49] chunk 151 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 74 ASN D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.296431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.282639 restraints weight = 16101.109| |-----------------------------------------------------------------------------| r_work (start): 0.4940 rms_B_bonded: 1.95 r_work: 0.4837 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13820 Z= 0.118 Angle : 0.589 7.774 18796 Z= 0.298 Chirality : 0.044 0.150 2104 Planarity : 0.005 0.041 2476 Dihedral : 7.637 103.304 2060 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.26 % Rotamer: Outliers : 5.77 % Allowed : 20.58 % Favored : 73.65 % 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: -1.67 (0.19), residues: 1824 helix: -0.28 (0.19), residues: 696 sheet: -1.65 (0.34), residues: 220 loop : -1.59 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.025 0.002 TYR A 314 PHE 0.016 0.002 PHE B 316 TRP 0.006 0.001 TRP B 143 HIS 0.003 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13820) covalent geometry : angle 0.58948 / 0.30 (18796) hydrogen bonds : bond 0.03051 / 2.11 ( 447) hydrogen bonds : angle 5.19142 / 3.65 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 223 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6716 (pt0) cc_final: 0.6321 (mp10) REVERT: A 35 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6290 (mm-30) REVERT: A 37 LEU cc_start: 0.7779 (mm) cc_final: 0.7506 (tp) REVERT: A 219 ARG cc_start: 0.6558 (ttp-170) cc_final: 0.5471 (ttp-170) REVERT: A 378 MET cc_start: 0.6651 (ptp) cc_final: 0.6055 (ppp) REVERT: A 385 SER cc_start: 0.6885 (t) cc_final: 0.6542 (m) REVERT: A 441 GLU cc_start: 0.7201 (mp0) cc_final: 0.6981 (mp0) REVERT: A 448 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5812 (tt) REVERT: B 37 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7519 (mm) REVERT: B 242 GLU cc_start: 0.6767 (pp20) cc_final: 0.6367 (pt0) REVERT: B 357 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6260 (mt) REVERT: C 5 GLN cc_start: 0.6653 (pt0) cc_final: 0.6259 (mp10) REVERT: C 37 LEU cc_start: 0.7691 (mm) cc_final: 0.7355 (tp) REVERT: C 219 ARG cc_start: 0.6677 (ttp-170) cc_final: 0.5703 (ttp-170) REVERT: C 242 GLU cc_start: 0.6669 (pp20) cc_final: 0.6324 (pt0) REVERT: C 260 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6735 (mtt-85) REVERT: C 279 LYS cc_start: 0.7002 (tmtt) cc_final: 0.6063 (ptpp) REVERT: C 385 SER cc_start: 0.6548 (t) cc_final: 0.6288 (m) REVERT: D 219 ARG cc_start: 0.6710 (ttp-170) cc_final: 0.5669 (ttp-170) REVERT: D 279 LYS cc_start: 0.7049 (tmtt) cc_final: 0.6398 (ttmm) outliers start: 81 outliers final: 60 residues processed: 283 average time/residue: 0.1223 time to fit residues: 49.4513 Evaluate side-chains 272 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 208 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 260 ARG Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 404 ASP Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [85, 147, 110, 55, 37, 122, 130, 75, 14, 60, 108] chunk 85 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 110 optimal weight: 0.0980 chunk 55 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.304555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.290044 restraints weight = 16411.784| |-----------------------------------------------------------------------------| r_work (start): 0.4987 rms_B_bonded: 2.11 r_work: 0.4878 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13820 Z= 0.095 Angle : 0.549 9.608 18796 Z= 0.277 Chirality : 0.043 0.155 2104 Planarity : 0.005 0.041 2476 Dihedral : 7.364 109.350 2060 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 3.85 % Allowed : 22.79 % Favored : 73.36 % 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: -1.37 (0.19), residues: 1824 helix: 0.15 (0.20), residues: 684 sheet: -1.51 (0.35), residues: 220 loop : -1.57 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.019 0.001 TYR A 314 PHE 0.016 0.001 PHE B 316 TRP 0.008 0.001 TRP C 143 HIS 0.003 0.001 HIS D 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (13820) covalent geometry : angle 0.54910 / 0.28 (18796) hydrogen bonds : bond 0.02736 / 1.86 ( 447) hydrogen bonds : angle 5.07410 / 3.56 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6638 (pt0) cc_final: 0.6238 (mp10) REVERT: A 37 LEU cc_start: 0.7727 (mm) cc_final: 0.7497 (tp) REVERT: A 219 ARG cc_start: 0.6360 (ttp-170) cc_final: 0.5287 (ttp-170) REVERT: A 378 MET cc_start: 0.6481 (ptp) cc_final: 0.5761 (ppp) REVERT: A 416 MET cc_start: 0.2911 (ptp) cc_final: 0.2686 (mmm) REVERT: B 242 GLU cc_start: 0.6849 (pp20) cc_final: 0.6497 (pt0) REVERT: B 410 MET cc_start: 0.6527 (ptp) cc_final: 0.6074 (mtm) REVERT: C 5 GLN cc_start: 0.6724 (pt0) cc_final: 0.6175 (mp10) REVERT: C 37 LEU cc_start: 0.7668 (mm) cc_final: 0.7342 (tp) REVERT: C 219 ARG cc_start: 0.6543 (ttp-170) cc_final: 0.5623 (ttp-170) REVERT: C 242 GLU cc_start: 0.6753 (pp20) cc_final: 0.6402 (pt0) REVERT: C 385 SER cc_start: 0.6282 (t) cc_final: 0.6063 (m) REVERT: D 219 ARG cc_start: 0.6559 (ttp-170) cc_final: 0.5533 (ttp-170) outliers start: 54 outliers final: 40 residues processed: 253 average time/residue: 0.1229 time to fit residues: 44.7781 Evaluate side-chains 229 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 448 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [164, 12, 50, 124, 14, 81, 61, 142, 83, 57, 29] chunk 164 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.298634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.283856 restraints weight = 16125.748| |-----------------------------------------------------------------------------| r_work (start): 0.4951 rms_B_bonded: 2.12 r_work: 0.4840 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13820 Z= 0.113 Angle : 0.572 9.665 18796 Z= 0.288 Chirality : 0.044 0.138 2104 Planarity : 0.005 0.039 2476 Dihedral : 7.481 102.957 2059 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 4.27 % Allowed : 22.58 % Favored : 73.15 % 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: -1.35 (0.19), residues: 1824 helix: 0.07 (0.19), residues: 696 sheet: -1.45 (0.35), residues: 220 loop : -1.50 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.018 0.002 TYR D 36 PHE 0.016 0.002 PHE A 316 TRP 0.006 0.001 TRP B 143 HIS 0.003 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (13820) covalent geometry : angle 0.57189 / 0.29 (18796) hydrogen bonds : bond 0.02825 / 1.96 ( 447) hydrogen bonds : angle 5.07279 / 3.57 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6744 (pt0) cc_final: 0.6324 (mp10) REVERT: A 37 LEU cc_start: 0.7773 (mm) cc_final: 0.7509 (tp) REVERT: A 219 ARG cc_start: 0.6531 (ttp-170) cc_final: 0.5334 (ttp-170) REVERT: A 378 MET cc_start: 0.6644 (ptp) cc_final: 0.5890 (ppp) REVERT: A 414 LEU cc_start: 0.7471 (mt) cc_final: 0.6588 (mp) REVERT: B 170 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5991 (tp30) REVERT: B 242 GLU cc_start: 0.6870 (pp20) cc_final: 0.6542 (pt0) REVERT: B 357 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6278 (mt) REVERT: B 410 MET cc_start: 0.6657 (ptp) cc_final: 0.6093 (mtm) REVERT: C 5 GLN cc_start: 0.6789 (pt0) cc_final: 0.6275 (mp10) REVERT: C 37 LEU cc_start: 0.7689 (mm) cc_final: 0.7310 (tp) REVERT: C 219 ARG cc_start: 0.6629 (ttp-170) cc_final: 0.5644 (ttp-170) REVERT: C 242 GLU cc_start: 0.6870 (pp20) cc_final: 0.6453 (pt0) REVERT: D 219 ARG cc_start: 0.6618 (ttp-170) cc_final: 0.5598 (ttp-170) REVERT: D 279 LYS cc_start: 0.7111 (tmtt) cc_final: 0.6258 (ttmm) REVERT: D 322 ASP cc_start: 0.7215 (m-30) cc_final: 0.7008 (m-30) REVERT: D 433 TRP cc_start: 0.6973 (m100) cc_final: 0.6713 (m100) outliers start: 60 outliers final: 46 residues processed: 256 average time/residue: 0.1318 time to fit residues: 47.2740 Evaluate side-chains 245 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 128 TYR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 448 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [1, 140, 32, 27, 105, 149, 129, 95, 74, 11, 46] chunk 1 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 0.0010 chunk 129 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5149 r_free = 0.5149 target = 0.305717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5022 r_free = 0.5022 target = 0.292342 restraints weight = 16227.510| |-----------------------------------------------------------------------------| r_work (start): 0.5052 rms_B_bonded: 1.92 r_work: 0.4947 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.4947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13820 Z= 0.095 Angle : 0.556 11.656 18796 Z= 0.278 Chirality : 0.043 0.141 2104 Planarity : 0.005 0.039 2476 Dihedral : 7.382 110.686 2058 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 2.85 % Allowed : 24.93 % Favored : 72.22 % 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: -1.14 (0.19), residues: 1824 helix: 0.26 (0.20), residues: 696 sheet: -1.30 (0.35), residues: 220 loop : -1.41 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.016 0.001 TYR D 36 PHE 0.021 0.001 PHE C 316 TRP 0.008 0.001 TRP D 433 HIS 0.003 0.001 HIS D 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (13820) covalent geometry : angle 0.55630 / 0.28 (18796) hydrogen bonds : bond 0.02731 / 1.86 ( 447) hydrogen bonds : angle 5.05829 / 3.54 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6639 (pt0) cc_final: 0.6288 (mp10) REVERT: A 107 ILE cc_start: 0.7737 (pt) cc_final: 0.7315 (tp) REVERT: A 219 ARG cc_start: 0.6253 (ttp-170) cc_final: 0.5239 (ttp-170) REVERT: A 378 MET cc_start: 0.6417 (ptp) cc_final: 0.5822 (ppp) REVERT: A 414 LEU cc_start: 0.7029 (mt) cc_final: 0.6241 (mp) REVERT: B 242 GLU cc_start: 0.6892 (pp20) cc_final: 0.6484 (pt0) REVERT: B 410 MET cc_start: 0.6447 (ptp) cc_final: 0.6050 (mtm) REVERT: C 5 GLN cc_start: 0.6659 (pt0) cc_final: 0.6209 (mp10) REVERT: C 37 LEU cc_start: 0.7677 (mm) cc_final: 0.7322 (tp) REVERT: C 219 ARG cc_start: 0.6215 (ttp-170) cc_final: 0.5413 (ttp-170) REVERT: C 242 GLU cc_start: 0.6753 (pp20) cc_final: 0.6355 (pt0) REVERT: C 311 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.7091 (ttp) REVERT: D 219 ARG cc_start: 0.6412 (ttp-170) cc_final: 0.5490 (ttp-170) outliers start: 40 outliers final: 36 residues processed: 238 average time/residue: 0.1229 time to fit residues: 41.9030 Evaluate side-chains 219 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 448 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [113, 169, 108, 119, 154, 99, 36, 144, 160, 21, 152] chunk 113 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 154 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 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 = 0.5121 r_free = 0.5121 target = 0.301753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.288512 restraints weight = 16130.688| |-----------------------------------------------------------------------------| r_work (start): 0.5001 rms_B_bonded: 1.85 r_work: 0.4898 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work (final): 0.4898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13820 Z= 0.113 Angle : 0.579 11.632 18796 Z= 0.291 Chirality : 0.043 0.142 2104 Planarity : 0.005 0.038 2476 Dihedral : 7.394 104.510 2057 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 2.99 % Allowed : 24.79 % Favored : 72.22 % 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: -1.08 (0.19), residues: 1824 helix: 0.29 (0.20), residues: 696 sheet: -1.24 (0.35), residues: 212 loop : -1.36 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 86 TYR 0.023 0.002 TYR D 314 PHE 0.018 0.002 PHE D 316 TRP 0.009 0.001 TRP D 143 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (13820) covalent geometry : angle 0.57937 / 0.29 (18796) hydrogen bonds : bond 0.02870 / 1.99 ( 447) hydrogen bonds : angle 4.98329 / 3.49 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.490 Fit side-chains REVERT: A 5 GLN cc_start: 0.6701 (pt0) cc_final: 0.6393 (mp10) REVERT: A 107 ILE cc_start: 0.7835 (pt) cc_final: 0.7526 (mt) REVERT: A 219 ARG cc_start: 0.6436 (ttp-170) cc_final: 0.5374 (ttp-170) REVERT: A 378 MET cc_start: 0.6390 (ptp) cc_final: 0.5846 (ppp) REVERT: B 242 GLU cc_start: 0.6830 (pp20) cc_final: 0.6410 (pt0) REVERT: C 5 GLN cc_start: 0.6700 (pt0) cc_final: 0.6309 (mp10) REVERT: C 37 LEU cc_start: 0.7785 (mm) cc_final: 0.7499 (tp) REVERT: C 219 ARG cc_start: 0.6398 (ttp-170) cc_final: 0.5448 (ttp-170) REVERT: C 242 GLU cc_start: 0.6764 (pp20) cc_final: 0.6360 (pt0) REVERT: C 321 LEU cc_start: 0.6120 (tp) cc_final: 0.5903 (tp) REVERT: D 219 ARG cc_start: 0.6534 (ttp-170) cc_final: 0.5557 (ttp-170) REVERT: D 322 ASP cc_start: 0.7255 (m-30) cc_final: 0.7046 (m-30) outliers start: 42 outliers final: 40 residues processed: 229 average time/residue: 0.1268 time to fit residues: 41.0530 Evaluate side-chains 228 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 443 LYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 407 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 448 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [115, 88, 174, 9, 102, 154, 91, 33, 80, 81, 75] chunk 115 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 0.0010 chunk 80 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 367 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 = 0.5131 r_free = 0.5131 target = 0.303177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.289822 restraints weight = 16077.392| |-----------------------------------------------------------------------------| r_work (start): 0.4996 rms_B_bonded: 1.87 r_work: 0.4893 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.4893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13820 Z= 0.100 Angle : 0.571 12.414 18796 Z= 0.285 Chirality : 0.043 0.141 2104 Planarity : 0.005 0.038 2476 Dihedral : 7.389 107.793 2057 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Rotamer: Outliers : 3.13 % Allowed : 25.57 % Favored : 71.30 % 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: -1.00 (0.19), residues: 1824 helix: 0.40 (0.20), residues: 696 sheet: -1.19 (0.35), residues: 212 loop : -1.37 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 103 TYR 0.017 0.001 TYR D 36 PHE 0.018 0.001 PHE B 316 TRP 0.006 0.001 TRP D 143 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (13820) covalent geometry : angle 0.57149 / 0.29 (18796) hydrogen bonds : bond 0.02773 / 1.95 ( 447) hydrogen bonds : angle 4.97936 / 3.47 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.18 seconds wall clock time: 43 minutes 57.40 seconds (2637.40 seconds total)