Starting phenix.real_space_refine on Sat Jun 6 09:28:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u7o_63941/06_2026/9u7o_63941_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u7o_63941/06_2026/9u7o_63941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u7o_63941/06_2026/9u7o_63941_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u7o_63941/06_2026/9u7o_63941_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u7o_63941/06_2026/9u7o_63941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u7o_63941/06_2026/9u7o_63941.map" } resolution = 3.96 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= 0.027 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: 6 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 H 13360 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26908 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 6706 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "B" Number of atoms: 6706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 6706 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "C" Number of atoms: 6706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 6706 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 29, 'TRANS': 428} Chain: "D" Number of atoms: 6706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 6706 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: 5.49, per 1000 atoms: 0.20 Number of scatterers: 26908 At special positions: 0 Unit cell: (81.88, 146.28, 89.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 4 15.00 O 2652 8.00 N 2340 7.00 C 8492 6.00 H 13360 1.00 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: 2.21 Conformation dependent library (CDL) restraints added in 879.9 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: 72 helices and 20 sheets defined 41.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 4.061A pdb=" N ILE A 11 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.583A pdb=" N ALA A 48 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 removed outlier: 5.003A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.877A 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 Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.618A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.949A pdb=" N ILE A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 195 through 198 removed outlier: 3.528A 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 248 through 263 removed outlier: 3.544A pdb=" N ASP A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 3.752A pdb=" N MET A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.625A pdb=" N TYR A 314 " --> pdb=" O TRP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.840A 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: 4.330A pdb=" N PHE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 430 Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'B' and resid 6 through 11 removed outlier: 4.053A pdb=" N ILE B 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.564A pdb=" N GLY B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.769A pdb=" N ARG B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.905A 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 Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.639A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.641A 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 Processing helix chain 'B' and resid 248 through 263 removed outlier: 3.539A pdb=" N ASP B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 284 removed outlier: 3.668A pdb=" N GLY B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.630A pdb=" N TYR B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.997A 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: 4.401A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.848A pdb=" N ALA B 408 " --> pdb=" O ALA B 405 " (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: 4.062A pdb=" N ILE C 11 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.671A pdb=" N ALA C 48 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 removed outlier: 4.105A pdb=" N GLY C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.502A pdb=" N ASN C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.529A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.703A 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 196 removed outlier: 3.959A pdb=" N GLY C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 263 removed outlier: 3.565A pdb=" N ASP C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 254 " --> pdb=" O ASP C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 284 removed outlier: 3.611A pdb=" N GLY C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 282 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 283 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 284 " --> pdb=" O VAL C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.622A pdb=" N TYR C 314 " --> pdb=" O TRP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 removed outlier: 3.857A 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: 4.353A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.799A pdb=" N ALA C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 430 Processing helix chain 'C' and resid 450 through 460 Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.085A pdb=" N ILE D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.893A pdb=" N ALA D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 87 removed outlier: 5.142A pdb=" N LEU D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.922A 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 Processing helix chain 'D' and resid 151 through 161 removed outlier: 3.549A pdb=" N ALA D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.729A 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 196 removed outlier: 3.860A pdb=" N GLY D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 263 removed outlier: 3.549A pdb=" N ASP D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 284 removed outlier: 5.142A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 284 " --> pdb=" O VAL D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.614A pdb=" N TYR D 314 " --> pdb=" O TRP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 336 removed outlier: 3.947A 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: 4.339A pdb=" N PHE D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 409 removed outlier: 3.839A pdb=" N ALA D 408 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 430 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: 6.187A pdb=" N ILE A 67 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 5.803A pdb=" N GLY A 205 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 246 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP A 207 " --> pdb=" O VAL A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.597A pdb=" N GLY A 384 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 417 removed outlier: 6.652A pdb=" N LEU A 436 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 447 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 438 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.783A pdb=" N LEU B 294 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 113 removed outlier: 6.206A pdb=" N ILE B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 208 removed outlier: 5.812A pdb=" N GLY B 205 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 246 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 370 removed outlier: 3.738A pdb=" N GLY B 384 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 416 through 417 removed outlier: 6.510A pdb=" N ILE B 417 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 436 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL B 447 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL B 438 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.784A pdb=" N LEU C 294 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.659A pdb=" N GLU C 69 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP C 143 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 205 through 208 removed outlier: 5.768A pdb=" N GLY C 205 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 246 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP C 207 " --> pdb=" O VAL C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.715A pdb=" N GLY C 384 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 416 through 417 removed outlier: 6.703A pdb=" N LEU C 436 " --> pdb=" O VAL C 447 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL C 447 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 438 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.895A pdb=" N LEU D 294 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.309A pdb=" N THR D 66 " --> pdb=" O TRP D 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 205 through 208 removed outlier: 5.777A pdb=" N GLY D 205 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL D 246 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASP D 207 " --> pdb=" O VAL D 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 367 through 370 removed outlier: 3.520A pdb=" N VAL D 370 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 384 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 417 removed outlier: 6.724A pdb=" N LEU D 436 " --> pdb=" O VAL D 447 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL D 447 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 438 " --> pdb=" O VAL D 445 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 13344 1.05 - 1.27: 2364 1.27 - 1.49: 5475 1.49 - 1.70: 5889 1.70 - 1.92: 108 Bond restraints: 27180 Sorted by residual: bond pdb=" O4P IK2 D 501 " pdb=" P IK2 D 501 " ideal model delta sigma weight residual 1.682 1.917 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" O4P IK2 A 501 " pdb=" P IK2 A 501 " ideal model delta sigma weight residual 1.682 1.906 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" O4P IK2 B 501 " pdb=" P IK2 B 501 " ideal model delta sigma weight residual 1.682 1.900 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" O4P IK2 C 501 " pdb=" P IK2 C 501 " ideal model delta sigma weight residual 1.682 1.884 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C4A IK2 A 501 " pdb=" N4A IK2 A 501 " ideal model delta sigma weight residual 1.474 1.572 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 27175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 43724 1.64 - 3.27: 5033 3.27 - 4.91: 388 4.91 - 6.54: 86 6.54 - 8.18: 9 Bond angle restraints: 49240 Sorted by residual: angle pdb=" N THR A 187 " pdb=" CA THR A 187 " pdb=" C THR A 187 " ideal model delta sigma weight residual 112.93 107.81 5.12 1.33e+00 5.65e-01 1.48e+01 angle pdb=" CA THR A 185 " pdb=" CB THR A 185 " pdb=" OG1 THR A 185 " ideal model delta sigma weight residual 109.60 104.13 5.47 1.50e+00 4.44e-01 1.33e+01 angle pdb=" CA THR A 187 " pdb=" CB THR A 187 " pdb=" OG1 THR A 187 " ideal model delta sigma weight residual 109.60 104.28 5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" N CYS A 270 " pdb=" CA CYS A 270 " pdb=" C CYS A 270 " ideal model delta sigma weight residual 112.68 108.91 3.77 1.33e+00 5.65e-01 8.04e+00 angle pdb=" C1' IK2 D 501 " pdb=" C2' IK2 D 501 " pdb=" O1' IK2 D 501 " ideal model delta sigma weight residual 113.61 121.79 -8.18 3.00e+00 1.11e-01 7.43e+00 ... (remaining 49235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 12254 31.29 - 62.58: 563 62.58 - 93.88: 8 93.88 - 125.17: 0 125.17 - 156.46: 3 Dihedral angle restraints: 12828 sinusoidal: 7128 harmonic: 5700 Sorted by residual: dihedral pdb=" C5 IK2 B 501 " pdb=" C4 IK2 B 501 " pdb=" C4A IK2 B 501 " pdb=" N4A IK2 B 501 " ideal model delta sinusoidal sigma weight residual 227.73 71.27 156.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C5 IK2 A 501 " pdb=" C4 IK2 A 501 " pdb=" C4A IK2 A 501 " pdb=" N4A IK2 A 501 " ideal model delta sinusoidal sigma weight residual 227.73 71.27 156.46 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C5 IK2 D 501 " pdb=" C4 IK2 D 501 " pdb=" C4A IK2 D 501 " pdb=" N4A IK2 D 501 " ideal model delta sinusoidal sigma weight residual 227.73 71.98 155.75 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 12825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1236 0.028 - 0.057: 516 0.057 - 0.085: 217 0.085 - 0.114: 119 0.114 - 0.142: 16 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 67 " pdb=" N ILE A 67 " pdb=" C ILE A 67 " pdb=" CB ILE A 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 2101 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 182 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C THR A 182 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 182 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY A 183 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 268 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C GLY A 268 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY A 268 " -0.009 2.00e-02 2.50e+03 pdb=" N SER A 269 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 69 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO D 70 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 70 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 70 " -0.016 5.00e-02 4.00e+02 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.93: 549 1.93 - 2.60: 30200 2.60 - 3.27: 82659 3.27 - 3.93: 100121 3.93 - 4.60: 156079 Nonbonded interactions: 369608 Sorted by model distance: nonbonded pdb=" O ILE C 165 " pdb=" HG1 THR C 169 " model vdw 1.264 2.450 nonbonded pdb=" O ILE A 165 " pdb=" HG1 THR A 169 " model vdw 1.269 2.450 nonbonded pdb=" O ILE B 165 " pdb=" HG1 THR B 169 " model vdw 1.273 2.450 nonbonded pdb=" O ILE D 165 " pdb=" HG1 THR D 169 " model vdw 1.276 2.450 nonbonded pdb=" O GLY A 73 " pdb=" HZ2 LYS A 102 " model vdw 1.303 2.450 ... (remaining 369603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 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: 0.180 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.270 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 13820 Z= 0.265 Angle : 0.572 8.176 18796 Z= 0.284 Chirality : 0.041 0.142 2104 Planarity : 0.003 0.029 2476 Dihedral : 11.693 156.462 5052 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 34.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.55 % Favored : 91.28 % Rotamer: Outliers : 6.91 % Allowed : 11.40 % Favored : 81.70 % 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: -2.08 (0.20), residues: 1824 helix: -0.60 (0.22), residues: 608 sheet: -1.92 (0.37), residues: 232 loop : -1.75 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 354 TYR 0.011 0.001 TYR B 36 PHE 0.008 0.001 PHE B 316 TRP 0.005 0.001 TRP D 166 HIS 0.002 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.26 (13820) covalent geometry : angle 0.57192 / 0.28 (18796) hydrogen bonds : bond 0.28593 / 19.81 ( 466) hydrogen bonds : angle 9.39061 / 6.62 ( 1311) *********************** 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 508 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 411 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 VAL cc_start: 0.7705 (t) cc_final: 0.7412 (t) REVERT: A 166 TRP cc_start: 0.6232 (t-100) cc_final: 0.5282 (t60) REVERT: A 289 LEU cc_start: 0.6964 (tt) cc_final: 0.6127 (tp) REVERT: A 293 LEU cc_start: 0.7797 (tp) cc_final: 0.7549 (tt) REVERT: A 368 MET cc_start: 0.8387 (ptp) cc_final: 0.7963 (ptt) REVERT: B 74 ASN cc_start: 0.8126 (m-40) cc_final: 0.7759 (m-40) REVERT: B 107 ILE cc_start: 0.8204 (mt) cc_final: 0.8004 (tp) REVERT: B 166 TRP cc_start: 0.6189 (t-100) cc_final: 0.5132 (t60) REVERT: B 289 LEU cc_start: 0.6853 (tt) cc_final: 0.6127 (tp) REVERT: B 368 MET cc_start: 0.8255 (ptm) cc_final: 0.7526 (ptm) REVERT: C 103 ARG cc_start: 0.7048 (ptt-90) cc_final: 0.6797 (ttm110) REVERT: C 150 ASN cc_start: 0.8295 (t0) cc_final: 0.7952 (p0) REVERT: C 166 TRP cc_start: 0.6285 (t-100) cc_final: 0.5253 (t60) REVERT: C 289 LEU cc_start: 0.6762 (tt) cc_final: 0.6043 (tp) REVERT: C 368 MET cc_start: 0.8250 (ptm) cc_final: 0.7986 (ptm) REVERT: C 437 MET cc_start: 0.7180 (ttp) cc_final: 0.6908 (ttp) REVERT: D 96 ASP cc_start: 0.7171 (m-30) cc_final: 0.6951 (t0) REVERT: D 107 ILE cc_start: 0.8244 (mt) cc_final: 0.7993 (tp) REVERT: D 166 TRP cc_start: 0.6228 (t-100) cc_final: 0.5303 (t60) REVERT: D 289 LEU cc_start: 0.6886 (tt) cc_final: 0.6166 (tp) outliers start: 97 outliers final: 37 residues processed: 477 average time/residue: 0.3245 time to fit residues: 208.2717 Evaluate side-chains 301 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN B 20 ASN C 20 ASN C 60 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.157064 restraints weight = 55572.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163738 restraints weight = 26787.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168223 restraints weight = 16108.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.171237 restraints weight = 11186.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173353 restraints weight = 8521.658| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13820 Z= 0.167 Angle : 0.684 7.322 18796 Z= 0.356 Chirality : 0.046 0.156 2104 Planarity : 0.005 0.058 2476 Dihedral : 9.858 164.181 2116 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 5.98 % Allowed : 17.66 % Favored : 76.35 % 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: -2.58 (0.18), residues: 1824 helix: -1.28 (0.17), residues: 700 sheet: -1.78 (0.41), residues: 184 loop : -2.02 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 361 TYR 0.014 0.001 TYR D 128 PHE 0.010 0.001 PHE B 316 TRP 0.008 0.001 TRP D 166 HIS 0.005 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (13820) covalent geometry : angle 0.68423 / 0.36 (18796) hydrogen bonds : bond 0.06364 / 4.59 ( 466) hydrogen bonds : angle 6.75161 / 4.77 ( 1311) *********************** 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 364 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 280 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.5515 (t-100) cc_final: 0.4551 (t60) REVERT: A 289 LEU cc_start: 0.7058 (tt) cc_final: 0.6296 (tp) REVERT: A 368 MET cc_start: 0.7837 (ptp) cc_final: 0.7476 (ptt) REVERT: B 166 TRP cc_start: 0.5533 (t-100) cc_final: 0.4563 (t60) REVERT: B 368 MET cc_start: 0.7812 (ptm) cc_final: 0.7495 (ptm) REVERT: C 150 ASN cc_start: 0.8154 (t0) cc_final: 0.7865 (p0) REVERT: C 166 TRP cc_start: 0.5592 (t-100) cc_final: 0.4407 (t60) REVERT: C 346 HIS cc_start: 0.6447 (p-80) cc_final: 0.6201 (p90) REVERT: C 368 MET cc_start: 0.8086 (ptm) cc_final: 0.7522 (ptm) REVERT: D 74 ASN cc_start: 0.7630 (m-40) cc_final: 0.7409 (m-40) REVERT: D 166 TRP cc_start: 0.5583 (t-100) cc_final: 0.4659 (t60) REVERT: D 289 LEU cc_start: 0.7163 (tt) cc_final: 0.6619 (tp) REVERT: D 410 MET cc_start: 0.6990 (ppp) cc_final: 0.6232 (ptm) outliers start: 84 outliers final: 53 residues processed: 336 average time/residue: 0.2730 time to fit residues: 129.2503 Evaluate side-chains 276 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.181109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.151957 restraints weight = 57824.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.158392 restraints weight = 28918.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.162711 restraints weight = 17907.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.165642 restraints weight = 12664.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.167691 restraints weight = 9802.010| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13820 Z= 0.219 Angle : 0.675 7.051 18796 Z= 0.351 Chirality : 0.045 0.151 2104 Planarity : 0.005 0.055 2476 Dihedral : 9.324 163.024 2081 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.53 % Favored : 89.42 % Rotamer: Outliers : 5.13 % Allowed : 18.59 % Favored : 76.28 % 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: -2.64 (0.18), residues: 1824 helix: -1.31 (0.17), residues: 680 sheet: -2.27 (0.50), residues: 128 loop : -2.03 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 134 TYR 0.013 0.001 TYR B 36 PHE 0.013 0.002 PHE B 316 TRP 0.016 0.002 TRP A 166 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.22 (13820) covalent geometry : angle 0.67506 / 0.35 (18796) hydrogen bonds : bond 0.06108 / 4.41 ( 466) hydrogen bonds : angle 6.71241 / 4.76 ( 1311) *********************** 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 310 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 SER cc_start: 0.7442 (p) cc_final: 0.4219 (p) REVERT: A 166 TRP cc_start: 0.5479 (t-100) cc_final: 0.4251 (t60) REVERT: A 289 LEU cc_start: 0.7185 (tt) cc_final: 0.6419 (tp) REVERT: A 368 MET cc_start: 0.8066 (ptp) cc_final: 0.7669 (ptt) REVERT: B 368 MET cc_start: 0.8015 (ptm) cc_final: 0.7688 (ptm) REVERT: C 103 ARG cc_start: 0.6044 (ttm110) cc_final: 0.5414 (ptp-170) REVERT: C 368 MET cc_start: 0.8256 (ptm) cc_final: 0.7674 (ptm) REVERT: D 21 SER cc_start: 0.7404 (p) cc_final: 0.5826 (t) REVERT: D 166 TRP cc_start: 0.5515 (t-100) cc_final: 0.4355 (t60) REVERT: D 289 LEU cc_start: 0.7367 (tt) cc_final: 0.6810 (tp) outliers start: 72 outliers final: 61 residues processed: 291 average time/residue: 0.2340 time to fit residues: 100.7856 Evaluate side-chains 288 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 227 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 46 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.183329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155048 restraints weight = 56024.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.161662 restraints weight = 26948.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.166070 restraints weight = 16236.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.169069 restraints weight = 11275.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.171169 restraints weight = 8581.708| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4192 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= 0.135 Angle : 0.613 7.193 18796 Z= 0.313 Chirality : 0.043 0.144 2104 Planarity : 0.004 0.046 2476 Dihedral : 9.029 161.956 2076 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.61 % Favored : 91.34 % Rotamer: Outliers : 4.27 % Allowed : 19.80 % Favored : 75.93 % 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: -2.65 (0.18), residues: 1824 helix: -1.12 (0.18), residues: 700 sheet: -2.01 (0.41), residues: 184 loop : -2.20 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 134 TYR 0.011 0.001 TYR B 192 PHE 0.011 0.001 PHE B 316 TRP 0.008 0.001 TRP D 310 HIS 0.002 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13820) covalent geometry : angle 0.61349 / 0.31 (18796) hydrogen bonds : bond 0.05018 / 3.62 ( 466) hydrogen bonds : angle 6.21523 / 4.39 ( 1311) *********************** 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 300 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8116 (tptp) cc_final: 0.7792 (tppt) REVERT: A 166 TRP cc_start: 0.5447 (t-100) cc_final: 0.4323 (t60) REVERT: A 289 LEU cc_start: 0.7097 (tt) cc_final: 0.6476 (mm) REVERT: B 46 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7756 (mpp80) REVERT: B 166 TRP cc_start: 0.5632 (t-100) cc_final: 0.4558 (t60) REVERT: B 289 LEU cc_start: 0.6862 (tt) cc_final: 0.6241 (tp) REVERT: B 368 MET cc_start: 0.7830 (ptm) cc_final: 0.7552 (ptm) REVERT: C 289 LEU cc_start: 0.7111 (tt) cc_final: 0.6589 (tp) REVERT: C 346 HIS cc_start: 0.6578 (p-80) cc_final: 0.6317 (p90) REVERT: C 368 MET cc_start: 0.8148 (ptm) cc_final: 0.7629 (ptm) REVERT: D 166 TRP cc_start: 0.5504 (t-100) cc_final: 0.4430 (t60) REVERT: D 289 LEU cc_start: 0.7225 (tt) cc_final: 0.6702 (tp) outliers start: 60 outliers final: 47 residues processed: 277 average time/residue: 0.2197 time to fit residues: 92.6207 Evaluate side-chains 274 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 226 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 32 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.153168 restraints weight = 57368.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159659 restraints weight = 28353.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.164105 restraints weight = 17482.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.167093 restraints weight = 12315.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169187 restraints weight = 9496.282| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13820 Z= 0.150 Angle : 0.605 7.254 18796 Z= 0.309 Chirality : 0.043 0.138 2104 Planarity : 0.005 0.046 2476 Dihedral : 8.775 159.394 2069 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.25 % Favored : 89.64 % Rotamer: Outliers : 4.84 % Allowed : 20.01 % Favored : 75.14 % 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: -2.58 (0.18), residues: 1824 helix: -1.03 (0.18), residues: 712 sheet: -1.93 (0.41), residues: 184 loop : -2.23 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 431 TYR 0.010 0.001 TYR C 36 PHE 0.011 0.001 PHE B 316 TRP 0.007 0.001 TRP C 310 HIS 0.002 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (13820) covalent geometry : angle 0.60465 / 0.31 (18796) hydrogen bonds : bond 0.04631 / 3.35 ( 466) hydrogen bonds : angle 6.04125 / 4.28 ( 1311) *********************** 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 302 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8203 (tptp) cc_final: 0.7906 (tppt) REVERT: A 166 TRP cc_start: 0.5539 (t-100) cc_final: 0.4459 (t60) REVERT: A 289 LEU cc_start: 0.7172 (tt) cc_final: 0.6531 (mm) REVERT: A 411 SER cc_start: 0.2918 (OUTLIER) cc_final: 0.2393 (m) REVERT: B 46 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7751 (mpp80) REVERT: B 289 LEU cc_start: 0.6939 (tt) cc_final: 0.6306 (tp) REVERT: B 368 MET cc_start: 0.7859 (ptm) cc_final: 0.7640 (ptm) REVERT: C 289 LEU cc_start: 0.7100 (tt) cc_final: 0.6578 (tp) REVERT: C 368 MET cc_start: 0.8190 (ptm) cc_final: 0.7707 (ptm) REVERT: C 410 MET cc_start: 0.6906 (ppp) cc_final: 0.6447 (ppp) REVERT: C 443 LYS cc_start: 0.8641 (tmtt) cc_final: 0.8413 (tptp) REVERT: D 60 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6988 (pt0) REVERT: D 166 TRP cc_start: 0.5591 (t-100) cc_final: 0.4535 (t60) REVERT: D 289 LEU cc_start: 0.7152 (tt) cc_final: 0.6660 (tp) outliers start: 68 outliers final: 59 residues processed: 281 average time/residue: 0.2163 time to fit residues: 93.5548 Evaluate side-chains 288 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 226 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.180771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152428 restraints weight = 58155.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.158594 restraints weight = 29544.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.162766 restraints weight = 18534.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.165487 restraints weight = 13244.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167506 restraints weight = 10396.936| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13820 Z= 0.176 Angle : 0.620 6.812 18796 Z= 0.320 Chirality : 0.043 0.149 2104 Planarity : 0.005 0.047 2476 Dihedral : 8.784 156.900 2066 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.75 % Favored : 89.14 % Rotamer: Outliers : 5.20 % Allowed : 19.94 % Favored : 74.86 % 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: -2.46 (0.18), residues: 1824 helix: -1.02 (0.18), residues: 700 sheet: -2.37 (0.49), residues: 128 loop : -2.01 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 389 TYR 0.013 0.001 TYR D 36 PHE 0.013 0.001 PHE B 316 TRP 0.009 0.001 TRP A 166 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (13820) covalent geometry : angle 0.61950 / 0.32 (18796) hydrogen bonds : bond 0.04483 / 3.26 ( 466) hydrogen bonds : angle 5.99367 / 4.26 ( 1311) *********************** 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 302 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 229 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8157 (tptp) cc_final: 0.7813 (tppt) REVERT: A 166 TRP cc_start: 0.5507 (t-100) cc_final: 0.4416 (t60) REVERT: A 289 LEU cc_start: 0.7023 (tt) cc_final: 0.6388 (mm) REVERT: A 295 PRO cc_start: 0.8851 (Cg_endo) cc_final: 0.8468 (Cg_exo) REVERT: A 411 SER cc_start: 0.3158 (OUTLIER) cc_final: 0.2719 (m) REVERT: B 134 ARG cc_start: 0.6331 (mmt180) cc_final: 0.5272 (mtm180) REVERT: B 289 LEU cc_start: 0.6793 (tt) cc_final: 0.6110 (tp) REVERT: B 368 MET cc_start: 0.7840 (ptm) cc_final: 0.7608 (ptm) REVERT: B 411 SER cc_start: 0.3238 (OUTLIER) cc_final: 0.2683 (m) REVERT: C 289 LEU cc_start: 0.6948 (tt) cc_final: 0.6379 (tp) REVERT: C 368 MET cc_start: 0.8172 (ptm) cc_final: 0.7713 (ptm) REVERT: C 410 MET cc_start: 0.6791 (ppp) cc_final: 0.6404 (ppp) REVERT: D 166 TRP cc_start: 0.5535 (t-100) cc_final: 0.4503 (t60) REVERT: D 289 LEU cc_start: 0.7013 (tt) cc_final: 0.6496 (tp) outliers start: 73 outliers final: 65 residues processed: 286 average time/residue: 0.2155 time to fit residues: 94.8186 Evaluate side-chains 281 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152185 restraints weight = 57777.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.158339 restraints weight = 29227.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.162540 restraints weight = 18306.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.165419 restraints weight = 13046.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.167346 restraints weight = 10130.246| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13820 Z= 0.166 Angle : 0.615 6.721 18796 Z= 0.315 Chirality : 0.043 0.153 2104 Planarity : 0.005 0.046 2476 Dihedral : 8.676 153.959 2066 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.13 % Favored : 88.76 % Rotamer: Outliers : 5.56 % Allowed : 19.87 % Favored : 74.57 % 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: -2.66 (0.18), residues: 1824 helix: -1.07 (0.18), residues: 708 sheet: -2.80 (0.40), residues: 168 loop : -2.11 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.012 0.001 TYR D 36 PHE 0.012 0.001 PHE A 316 TRP 0.008 0.001 TRP A 166 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (13820) covalent geometry : angle 0.61458 / 0.32 (18796) hydrogen bonds : bond 0.04318 / 3.14 ( 466) hydrogen bonds : angle 5.89316 / 4.18 ( 1311) *********************** 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 299 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 221 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LYS cc_start: 0.8204 (tptp) cc_final: 0.7897 (tppt) REVERT: A 166 TRP cc_start: 0.5555 (t-100) cc_final: 0.4414 (t60) REVERT: A 289 LEU cc_start: 0.7028 (tt) cc_final: 0.6390 (mm) REVERT: A 295 PRO cc_start: 0.8823 (Cg_endo) cc_final: 0.8464 (Cg_exo) REVERT: A 332 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5563 (t0) REVERT: A 410 MET cc_start: 0.6702 (ppp) cc_final: 0.6308 (ppp) REVERT: A 411 SER cc_start: 0.3125 (OUTLIER) cc_final: 0.2365 (m) REVERT: B 21 SER cc_start: 0.7671 (m) cc_final: 0.6940 (t) REVERT: B 134 ARG cc_start: 0.6374 (mmt180) cc_final: 0.5296 (mtm180) REVERT: B 261 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: B 289 LEU cc_start: 0.6798 (tt) cc_final: 0.6109 (tp) REVERT: B 410 MET cc_start: 0.6705 (ppp) cc_final: 0.6270 (ppp) REVERT: B 411 SER cc_start: 0.3219 (OUTLIER) cc_final: 0.2413 (m) REVERT: C 289 LEU cc_start: 0.6941 (tt) cc_final: 0.6370 (tp) REVERT: C 368 MET cc_start: 0.8176 (ptm) cc_final: 0.7766 (ptm) REVERT: C 410 MET cc_start: 0.6718 (ppp) cc_final: 0.6359 (ptm) REVERT: D 166 TRP cc_start: 0.5626 (t-100) cc_final: 0.4587 (t60) REVERT: D 289 LEU cc_start: 0.7037 (tt) cc_final: 0.6501 (tp) REVERT: D 411 SER cc_start: 0.3253 (OUTLIER) cc_final: 0.2777 (m) outliers start: 78 outliers final: 65 residues processed: 283 average time/residue: 0.2112 time to fit residues: 92.6539 Evaluate side-chains 287 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 176 optimal weight: 0.0670 chunk 178 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.154266 restraints weight = 55827.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.160742 restraints weight = 26762.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165109 restraints weight = 16116.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168101 restraints weight = 11143.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170073 restraints weight = 8457.540| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13820 Z= 0.118 Angle : 0.588 6.845 18796 Z= 0.298 Chirality : 0.042 0.140 2104 Planarity : 0.005 0.046 2476 Dihedral : 8.398 152.909 2063 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.50 % Favored : 91.39 % Rotamer: Outliers : 4.34 % Allowed : 21.15 % Favored : 74.50 % 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: -2.40 (0.19), residues: 1824 helix: -0.84 (0.18), residues: 712 sheet: -2.67 (0.40), residues: 168 loop : -1.98 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 431 TYR 0.011 0.001 TYR B 192 PHE 0.011 0.001 PHE B 316 TRP 0.010 0.001 TRP D 310 HIS 0.003 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13820) covalent geometry : angle 0.58840 / 0.30 (18796) hydrogen bonds : bond 0.03981 / 2.87 ( 466) hydrogen bonds : angle 5.62598 / 3.99 ( 1311) *********************** 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 283 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TRP cc_start: 0.5539 (t-100) cc_final: 0.4404 (t60) REVERT: A 289 LEU cc_start: 0.7135 (tt) cc_final: 0.6469 (mm) REVERT: A 295 PRO cc_start: 0.8813 (Cg_endo) cc_final: 0.8480 (Cg_exo) REVERT: A 410 MET cc_start: 0.6686 (ppp) cc_final: 0.6313 (ppp) REVERT: A 411 SER cc_start: 0.2931 (OUTLIER) cc_final: 0.2108 (m) REVERT: B 21 SER cc_start: 0.7560 (m) cc_final: 0.6861 (t) REVERT: B 134 ARG cc_start: 0.6325 (mmt180) cc_final: 0.5228 (mtm180) REVERT: B 289 LEU cc_start: 0.6907 (tt) cc_final: 0.6205 (tp) REVERT: B 410 MET cc_start: 0.6612 (ppp) cc_final: 0.6196 (ppp) REVERT: B 411 SER cc_start: 0.2986 (OUTLIER) cc_final: 0.2130 (m) REVERT: C 289 LEU cc_start: 0.7068 (tt) cc_final: 0.6515 (tp) REVERT: C 368 MET cc_start: 0.8161 (ptm) cc_final: 0.7819 (ptm) REVERT: C 410 MET cc_start: 0.6642 (ppp) cc_final: 0.6231 (ptm) REVERT: C 411 SER cc_start: 0.3251 (OUTLIER) cc_final: 0.2751 (m) REVERT: D 166 TRP cc_start: 0.5640 (t-100) cc_final: 0.4621 (t60) REVERT: D 289 LEU cc_start: 0.7198 (tt) cc_final: 0.6703 (tp) REVERT: D 411 SER cc_start: 0.3097 (OUTLIER) cc_final: 0.2614 (m) outliers start: 61 outliers final: 54 residues processed: 270 average time/residue: 0.2094 time to fit residues: 87.7382 Evaluate side-chains 272 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 270 CYS Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 164 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.179674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151234 restraints weight = 58656.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.157357 restraints weight = 29893.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161506 restraints weight = 18763.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164343 restraints weight = 13447.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166286 restraints weight = 10503.046| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13820 Z= 0.183 Angle : 0.631 6.378 18796 Z= 0.325 Chirality : 0.043 0.150 2104 Planarity : 0.005 0.046 2476 Dihedral : 8.519 146.698 2063 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.06 % Favored : 87.83 % Rotamer: Outliers : 4.91 % Allowed : 20.73 % Favored : 74.36 % 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: -2.62 (0.18), residues: 1824 helix: -1.00 (0.18), residues: 708 sheet: -2.71 (0.40), residues: 168 loop : -2.13 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 399 TYR 0.014 0.001 TYR D 36 PHE 0.013 0.002 PHE B 316 TRP 0.010 0.001 TRP A 166 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (13820) covalent geometry : angle 0.63131 / 0.33 (18796) hydrogen bonds : bond 0.04294 / 3.12 ( 466) hydrogen bonds : angle 5.82833 / 4.15 ( 1311) *********************** 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 282 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 213 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.6171 (OUTLIER) cc_final: 0.5884 (m) REVERT: A 166 TRP cc_start: 0.5558 (t-100) cc_final: 0.4344 (t60) REVERT: A 289 LEU cc_start: 0.7064 (tt) cc_final: 0.6429 (mm) REVERT: A 295 PRO cc_start: 0.8889 (Cg_endo) cc_final: 0.8531 (Cg_exo) REVERT: A 332 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5604 (t0) REVERT: A 410 MET cc_start: 0.6686 (ppp) cc_final: 0.6307 (ppp) REVERT: A 411 SER cc_start: 0.3197 (OUTLIER) cc_final: 0.2424 (m) REVERT: B 21 SER cc_start: 0.7624 (m) cc_final: 0.7011 (t) REVERT: B 134 ARG cc_start: 0.6440 (mmt180) cc_final: 0.5377 (mtm180) REVERT: B 289 LEU cc_start: 0.6824 (tt) cc_final: 0.6102 (tp) REVERT: B 410 MET cc_start: 0.6650 (ppp) cc_final: 0.6213 (ptm) REVERT: B 411 SER cc_start: 0.3050 (OUTLIER) cc_final: 0.2505 (m) REVERT: C 289 LEU cc_start: 0.6943 (tt) cc_final: 0.6370 (tp) REVERT: C 368 MET cc_start: 0.8126 (ptm) cc_final: 0.7787 (ptm) REVERT: C 410 MET cc_start: 0.6712 (ppp) cc_final: 0.6318 (ptm) REVERT: C 411 SER cc_start: 0.3250 (OUTLIER) cc_final: 0.2739 (m) REVERT: D 289 LEU cc_start: 0.6994 (tt) cc_final: 0.6457 (tp) REVERT: D 411 SER cc_start: 0.3131 (OUTLIER) cc_final: 0.2659 (m) outliers start: 69 outliers final: 59 residues processed: 268 average time/residue: 0.2146 time to fit residues: 87.3390 Evaluate side-chains 272 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 39 optimal weight: 0.3980 chunk 177 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.152464 restraints weight = 56462.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.158769 restraints weight = 27336.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.163055 restraints weight = 16592.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165965 restraints weight = 11584.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.167989 restraints weight = 8853.749| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13820 Z= 0.145 Angle : 0.609 7.243 18796 Z= 0.310 Chirality : 0.043 0.145 2104 Planarity : 0.005 0.061 2476 Dihedral : 8.288 140.838 2059 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.76 % Favored : 90.13 % Rotamer: Outliers : 4.63 % Allowed : 21.08 % Favored : 74.29 % 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: -2.60 (0.18), residues: 1824 helix: -0.88 (0.18), residues: 708 sheet: -2.25 (0.34), residues: 224 loop : -2.28 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 256 TYR 0.012 0.001 TYR C 451 PHE 0.012 0.001 PHE B 316 TRP 0.009 0.001 TRP C 310 HIS 0.002 0.001 HIS D 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13820) covalent geometry : angle 0.60895 / 0.31 (18796) hydrogen bonds : bond 0.04015 / 2.90 ( 466) hydrogen bonds : angle 5.65819 / 4.02 ( 1311) ********************** 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 281 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 216 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.5918 (OUTLIER) cc_final: 0.5601 (m) REVERT: A 166 TRP cc_start: 0.5648 (t-100) cc_final: 0.4449 (t60) REVERT: A 289 LEU cc_start: 0.7227 (tt) cc_final: 0.6553 (mm) REVERT: A 295 PRO cc_start: 0.8869 (Cg_endo) cc_final: 0.8532 (Cg_exo) REVERT: A 332 ASP cc_start: 0.6054 (OUTLIER) cc_final: 0.5660 (t0) REVERT: A 411 SER cc_start: 0.3082 (OUTLIER) cc_final: 0.2600 (m) REVERT: B 21 SER cc_start: 0.7536 (m) cc_final: 0.6582 (t) REVERT: B 134 ARG cc_start: 0.6418 (mmt180) cc_final: 0.5332 (mtm180) REVERT: B 261 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: B 289 LEU cc_start: 0.6957 (tt) cc_final: 0.6239 (tp) REVERT: B 410 MET cc_start: 0.6586 (ppp) cc_final: 0.6154 (ptm) REVERT: B 411 SER cc_start: 0.3006 (OUTLIER) cc_final: 0.2455 (m) REVERT: C 289 LEU cc_start: 0.7105 (tt) cc_final: 0.6542 (tp) REVERT: C 368 MET cc_start: 0.8162 (ptm) cc_final: 0.7821 (ptm) REVERT: C 410 MET cc_start: 0.6651 (ppp) cc_final: 0.6250 (ptm) REVERT: C 411 SER cc_start: 0.3133 (OUTLIER) cc_final: 0.2623 (m) REVERT: D 166 TRP cc_start: 0.5683 (t-100) cc_final: 0.4590 (t60) REVERT: D 289 LEU cc_start: 0.7155 (tt) cc_final: 0.6624 (tp) REVERT: D 411 SER cc_start: 0.2998 (OUTLIER) cc_final: 0.2499 (m) outliers start: 65 outliers final: 56 residues processed: 267 average time/residue: 0.2416 time to fit residues: 97.7474 Evaluate side-chains 269 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 GLN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 303 SER Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 66 optimal weight: 0.1980 chunk 177 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154133 restraints weight = 57131.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.160709 restraints weight = 28033.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.165181 restraints weight = 17173.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.168179 restraints weight = 12068.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170272 restraints weight = 9325.486| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13820 Z= 0.110 Angle : 0.586 6.587 18796 Z= 0.295 Chirality : 0.042 0.135 2104 Planarity : 0.004 0.046 2476 Dihedral : 7.948 137.145 2059 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.55 % Favored : 91.39 % Rotamer: Outliers : 3.70 % Allowed : 22.15 % Favored : 74.15 % 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: -2.15 (0.19), residues: 1824 helix: -0.54 (0.19), residues: 696 sheet: -2.36 (0.47), residues: 128 loop : -1.98 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.013 0.001 TYR A 451 PHE 0.012 0.001 PHE A 396 TRP 0.011 0.001 TRP C 310 HIS 0.002 0.001 HIS C 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (13820) covalent geometry : angle 0.58586 / 0.29 (18796) hydrogen bonds : bond 0.03703 / 2.67 ( 466) hydrogen bonds : angle 5.38314 / 3.82 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4013.10 seconds wall clock time: 69 minutes 12.23 seconds (4152.23 seconds total)