Starting phenix.real_space_refine on Wed Mar 4 20:20:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wul_21915/03_2026/6wul_21915.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wul_21915/03_2026/6wul_21915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wul_21915/03_2026/6wul_21915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wul_21915/03_2026/6wul_21915.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wul_21915/03_2026/6wul_21915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wul_21915/03_2026/6wul_21915.map" } resolution = 3.2 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= 0.013 sd= 0.164 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 10400 2.51 5 N 2920 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16386 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2284 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 22, 'TRANS': 272} Chain breaks: 2 Chain: "B" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3295 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 22, 'TRANS': 420} Chain breaks: 3 Chain: "C" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2614 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain breaks: 3 Restraints were copied for chains: D, E, F Time building chain proxies: 4.69, per 1000 atoms: 0.29 Number of scatterers: 16386 At special positions: 0 Unit cell: (119.78, 155.82, 112.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 3036 8.00 N 2920 7.00 C 10400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 759.9 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 38.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.921A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.439A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 150 through 162 removed outlier: 3.926A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.890A pdb=" N SER A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 192' Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.331A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.879A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 286 removed outlier: 4.086A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.619A pdb=" N LEU B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'C' and resid 18 through 32 removed outlier: 3.612A pdb=" N LEU C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 4.039A pdb=" N VAL C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 121 removed outlier: 3.666A pdb=" N ALA C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.694A pdb=" N ALA C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.632A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 170 removed outlier: 3.600A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.830A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 284 removed outlier: 3.814A pdb=" N LEU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.574A pdb=" N CYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.546A pdb=" N GLY C 319 " --> pdb=" O PRO C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 Processing helix chain 'C' and resid 354 through 378 Processing helix chain 'C' and resid 386 through 408 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.921A pdb=" N ARG D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 removed outlier: 4.440A pdb=" N TRP D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.926A pdb=" N ALA D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 160 " --> pdb=" O TYR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 178 through 187 Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.891A pdb=" N SER D 191 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 193 through 213 removed outlier: 4.331A pdb=" N ALA D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.879A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 286 removed outlier: 4.087A pdb=" N TYR D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 311 through 321 Processing helix chain 'E' and resid 58 through 67 removed outlier: 3.619A pdb=" N LEU E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 79 through 94 Processing helix chain 'E' and resid 255 through 261 Processing helix chain 'E' and resid 446 through 463 Processing helix chain 'F' and resid 18 through 32 removed outlier: 3.612A pdb=" N LEU F 22 " --> pdb=" O ASP F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 47 removed outlier: 4.040A pdb=" N VAL F 47 " --> pdb=" O PRO F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.666A pdb=" N ALA F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 141 through 148 removed outlier: 3.694A pdb=" N ALA F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 156 removed outlier: 3.632A pdb=" N TRP F 156 " --> pdb=" O PRO F 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 153 through 156' Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.600A pdb=" N ALA F 161 " --> pdb=" O THR F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 254 removed outlier: 3.831A pdb=" N VAL F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL F 252 " --> pdb=" O GLU F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.813A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 300 Processing helix chain 'F' and resid 300 through 315 removed outlier: 3.575A pdb=" N CYS F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 320 removed outlier: 3.546A pdb=" N GLY F 319 " --> pdb=" O PRO F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'F' and resid 354 through 378 Processing helix chain 'F' and resid 386 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.802A pdb=" N PHE A 103 " --> pdb=" O TYR A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 109 removed outlier: 6.236A pdb=" N THR B 48 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE B 130 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU B 50 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.565A pdb=" N SER B 188 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU B 197 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B 309 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 345 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 340 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 236 removed outlier: 4.566A pdb=" N PHE B 309 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 345 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 340 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 401 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 421 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 471 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 206 through 210 removed outlier: 3.766A pdb=" N GLU B 217 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 215 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.103A pdb=" N ILE C 40 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU C 5 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 54 " --> pdb=" O HIS C 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 87 through 90 removed outlier: 3.802A pdb=" N PHE D 103 " --> pdb=" O TYR D 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 106 through 109 removed outlier: 6.236A pdb=" N THR E 48 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE E 130 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLU E 50 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 168 removed outlier: 3.565A pdb=" N SER E 188 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU E 197 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE E 309 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR E 345 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 314 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 339 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG E 340 " --> pdb=" O ALA E 398 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 235 through 236 removed outlier: 4.566A pdb=" N PHE E 309 " --> pdb=" O ALA E 298 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR E 345 " --> pdb=" O ALA E 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 314 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 339 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG E 340 " --> pdb=" O ALA E 398 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 401 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR E 421 " --> pdb=" O GLY E 471 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E 471 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 206 through 210 removed outlier: 3.766A pdb=" N GLU E 217 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS E 215 " --> pdb=" O LYS E 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 319 through 320 Processing sheet with id=AB5, first strand: chain 'F' and resid 40 through 41 removed outlier: 7.103A pdb=" N ILE F 40 " --> pdb=" O VAL F 3 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU F 5 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 54 " --> pdb=" O HIS F 6 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5455 1.34 - 1.46: 3084 1.46 - 1.57: 8175 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 16764 Sorted by residual: bond pdb=" C ALA B 357 " pdb=" N GLN B 358 " ideal model delta sigma weight residual 1.331 1.299 0.032 2.07e-02 2.33e+03 2.43e+00 bond pdb=" C ALA E 357 " pdb=" N GLN E 358 " ideal model delta sigma weight residual 1.331 1.300 0.031 2.07e-02 2.33e+03 2.31e+00 bond pdb=" CG LEU E 250 " pdb=" CD2 LEU E 250 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.90e+00 bond pdb=" CG LEU B 250 " pdb=" CD2 LEU B 250 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CA ALA B 207 " pdb=" C ALA B 207 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.08e-02 8.57e+03 1.74e+00 ... (remaining 16759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21726 1.69 - 3.37: 904 3.37 - 5.06: 134 5.06 - 6.75: 32 6.75 - 8.43: 12 Bond angle restraints: 22808 Sorted by residual: angle pdb=" C GLY B 193 " pdb=" N ASN B 194 " pdb=" CA ASN B 194 " ideal model delta sigma weight residual 121.61 130.04 -8.43 1.39e+00 5.18e-01 3.68e+01 angle pdb=" C GLY E 193 " pdb=" N ASN E 194 " pdb=" CA ASN E 194 " ideal model delta sigma weight residual 121.61 130.01 -8.40 1.39e+00 5.18e-01 3.65e+01 angle pdb=" N TYR D 32 " pdb=" CA TYR D 32 " pdb=" C TYR D 32 " ideal model delta sigma weight residual 110.44 116.86 -6.42 1.20e+00 6.94e-01 2.86e+01 angle pdb=" N TYR A 32 " pdb=" CA TYR A 32 " pdb=" C TYR A 32 " ideal model delta sigma weight residual 110.44 116.85 -6.41 1.20e+00 6.94e-01 2.85e+01 angle pdb=" N GLU D 258 " pdb=" CA GLU D 258 " pdb=" CB GLU D 258 " ideal model delta sigma weight residual 114.17 109.79 4.38 1.14e+00 7.69e-01 1.48e+01 ... (remaining 22803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 8724 16.73 - 33.46: 906 33.46 - 50.19: 226 50.19 - 66.92: 74 66.92 - 83.65: 22 Dihedral angle restraints: 9952 sinusoidal: 3810 harmonic: 6142 Sorted by residual: dihedral pdb=" CA PRO D 34 " pdb=" C PRO D 34 " pdb=" N ASN D 35 " pdb=" CA ASN D 35 " ideal model delta harmonic sigma weight residual -180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA PRO A 34 " pdb=" C PRO A 34 " pdb=" N ASN A 35 " pdb=" CA ASN A 35 " ideal model delta harmonic sigma weight residual -180.00 -149.06 -30.94 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ALA E 185 " pdb=" C ALA E 185 " pdb=" N THR E 186 " pdb=" CA THR E 186 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 9949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1650 0.037 - 0.074: 633 0.074 - 0.110: 211 0.110 - 0.147: 64 0.147 - 0.184: 6 Chirality restraints: 2564 Sorted by residual: chirality pdb=" CA LEU F 52 " pdb=" N LEU F 52 " pdb=" C LEU F 52 " pdb=" CB LEU F 52 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA THR E 186 " pdb=" N THR E 186 " pdb=" C THR E 186 " pdb=" CB THR E 186 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2561 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 124 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO C 125 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 124 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO F 125 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 125 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 125 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 355 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C PRO F 355 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO F 355 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU F 356 " 0.012 2.00e-02 2.50e+03 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 398 2.66 - 3.22: 14903 3.22 - 3.78: 23895 3.78 - 4.34: 32676 4.34 - 4.90: 55920 Nonbonded interactions: 127792 Sorted by model distance: nonbonded pdb=" O THR D 259 " pdb=" OG1 THR D 259 " model vdw 2.101 3.040 nonbonded pdb=" O THR A 259 " pdb=" OG1 THR A 259 " model vdw 2.101 3.040 nonbonded pdb=" OG SER D 41 " pdb=" OG1 THR E 257 " model vdw 2.174 3.040 nonbonded pdb=" OG1 THR A 57 " pdb=" OD2 ASP A 60 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR D 57 " pdb=" OD2 ASP D 60 " model vdw 2.191 3.040 ... (remaining 127787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.510 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 0.046 16764 Z= 0.237 Angle : 0.829 8.435 22808 Z= 0.476 Chirality : 0.045 0.184 2564 Planarity : 0.005 0.051 2962 Dihedral : 15.562 83.654 6012 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.71 % Favored : 87.19 % Rotamer: Outliers : 7.00 % Allowed : 13.58 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.16), residues: 2124 helix: -1.26 (0.17), residues: 764 sheet: -3.07 (0.23), residues: 388 loop : -3.46 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 163 TYR 0.010 0.001 TYR F 37 PHE 0.012 0.002 PHE E 396 TRP 0.012 0.002 TRP C 360 HIS 0.004 0.001 HIS E 215 Details of bonding type rmsd covalent geometry : bond 0.00520 (16764) covalent geometry : angle 0.82862 (22808) hydrogen bonds : bond 0.15909 ( 664) hydrogen bonds : angle 7.37216 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 212 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.8572 (tp) cc_final: 0.8256 (tp) REVERT: A 304 MET cc_start: 0.8231 (mtp) cc_final: 0.7945 (mtm) REVERT: B 99 ILE cc_start: 0.7577 (mt) cc_final: 0.7162 (mt) REVERT: B 137 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6764 (tmm160) REVERT: B 202 GLU cc_start: 0.7748 (tt0) cc_final: 0.7491 (tt0) REVERT: B 358 GLN cc_start: 0.8518 (mt0) cc_final: 0.8070 (mm-40) REVERT: B 467 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6944 (m) REVERT: B 485 LEU cc_start: 0.8026 (tt) cc_final: 0.7693 (mm) REVERT: C 247 ARG cc_start: 0.7274 (mtp85) cc_final: 0.6859 (ttt-90) REVERT: C 251 ASP cc_start: 0.7885 (m-30) cc_final: 0.7175 (m-30) REVERT: D 261 TRP cc_start: 0.8165 (m100) cc_final: 0.7880 (m100) REVERT: E 108 PHE cc_start: 0.7647 (m-80) cc_final: 0.7048 (m-10) REVERT: E 137 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6497 (tmm160) REVERT: E 202 GLU cc_start: 0.7781 (tt0) cc_final: 0.7545 (tt0) REVERT: E 358 GLN cc_start: 0.8505 (mt0) cc_final: 0.8076 (mm-40) REVERT: E 375 ARG cc_start: 0.7887 (mtt180) cc_final: 0.7559 (mtm180) REVERT: E 467 SER cc_start: 0.7362 (OUTLIER) cc_final: 0.7068 (m) REVERT: F 247 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6912 (ttt-90) REVERT: F 251 ASP cc_start: 0.7839 (m-30) cc_final: 0.7131 (m-30) outliers start: 118 outliers final: 75 residues processed: 323 average time/residue: 0.1550 time to fit residues: 70.2496 Evaluate side-chains 251 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 264 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 446 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 472 VAL Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 211 GLN A 310 ASN B 148 ASN B 286 GLN B 385 HIS B 431 ASN C 30 GLN C 51 HIS C 330 GLN D 69 ASN D 310 ASN E 148 ASN E 286 GLN E 385 HIS E 431 ASN F 30 GLN F 51 HIS F 330 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.162830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125601 restraints weight = 18949.664| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.15 r_work: 0.3202 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16764 Z= 0.266 Angle : 0.810 8.529 22808 Z= 0.408 Chirality : 0.049 0.212 2564 Planarity : 0.006 0.050 2962 Dihedral : 9.301 55.369 2475 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.38 % Favored : 87.48 % Rotamer: Outliers : 7.41 % Allowed : 14.53 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.93 (0.17), residues: 2124 helix: -0.31 (0.19), residues: 760 sheet: -2.68 (0.24), residues: 406 loop : -2.98 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 368 TYR 0.017 0.002 TYR A 32 PHE 0.020 0.002 PHE D 262 TRP 0.015 0.002 TRP F 360 HIS 0.005 0.001 HIS E 215 Details of bonding type rmsd covalent geometry : bond 0.00652 (16764) covalent geometry : angle 0.81018 (22808) hydrogen bonds : bond 0.05055 ( 664) hydrogen bonds : angle 5.13512 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 173 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7083 (mtp85) cc_final: 0.6857 (mtp85) REVERT: A 87 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7759 (ttp-170) REVERT: B 137 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6622 (tmm160) REVERT: B 160 ARG cc_start: 0.7450 (tpp-160) cc_final: 0.7176 (tpp-160) REVERT: B 202 GLU cc_start: 0.8338 (tt0) cc_final: 0.7989 (tt0) REVERT: B 358 GLN cc_start: 0.8595 (mt0) cc_final: 0.8321 (mm-40) REVERT: B 375 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7329 (mtm180) REVERT: B 467 SER cc_start: 0.7709 (OUTLIER) cc_final: 0.7222 (m) REVERT: B 503 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.4989 (pt) REVERT: C 52 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7328 (tm) REVERT: C 247 ARG cc_start: 0.7558 (mtp85) cc_final: 0.6950 (mtt-85) REVERT: C 251 ASP cc_start: 0.8276 (m-30) cc_final: 0.7473 (m-30) REVERT: D 30 ARG cc_start: 0.7267 (mtp85) cc_final: 0.7060 (mtp85) REVERT: D 49 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7894 (mt) REVERT: D 60 ASP cc_start: 0.7922 (m-30) cc_final: 0.7570 (m-30) REVERT: E 137 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6211 (tmm160) REVERT: E 160 ARG cc_start: 0.7446 (tpp-160) cc_final: 0.7179 (tpp-160) REVERT: E 202 GLU cc_start: 0.8280 (tt0) cc_final: 0.7998 (tt0) REVERT: E 358 GLN cc_start: 0.8596 (mt0) cc_final: 0.8373 (mm-40) REVERT: E 375 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7288 (mtm180) REVERT: E 467 SER cc_start: 0.7847 (OUTLIER) cc_final: 0.7120 (m) REVERT: E 468 LEU cc_start: 0.8470 (mt) cc_final: 0.8137 (mt) REVERT: E 503 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.4860 (pt) REVERT: F 52 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7326 (tm) REVERT: F 247 ARG cc_start: 0.7592 (mtp85) cc_final: 0.6994 (mtt-85) REVERT: F 251 ASP cc_start: 0.8236 (m-30) cc_final: 0.7431 (m-30) REVERT: F 311 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7579 (ttt180) outliers start: 125 outliers final: 83 residues processed: 287 average time/residue: 0.1395 time to fit residues: 57.7657 Evaluate side-chains 252 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 160 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 270 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 100 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 106 optimal weight: 0.0060 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS A 211 GLN C 30 GLN F 30 GLN F 172 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.168587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131018 restraints weight = 18807.982| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.28 r_work: 0.3299 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16764 Z= 0.119 Angle : 0.647 6.624 22808 Z= 0.328 Chirality : 0.043 0.158 2564 Planarity : 0.005 0.047 2962 Dihedral : 7.794 56.036 2434 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 4.86 % Allowed : 16.90 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.14 (0.18), residues: 2124 helix: 0.45 (0.20), residues: 764 sheet: -2.05 (0.26), residues: 390 loop : -2.75 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 426 TYR 0.012 0.001 TYR A 32 PHE 0.013 0.001 PHE D 262 TRP 0.010 0.001 TRP C 360 HIS 0.011 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00253 (16764) covalent geometry : angle 0.64656 (22808) hydrogen bonds : bond 0.03583 ( 664) hydrogen bonds : angle 4.64814 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 174 time to evaluate : 0.491 Fit side-chains REVERT: A 49 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7881 (mt) REVERT: A 87 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7663 (ttp-170) REVERT: A 206 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7557 (ttm170) REVERT: A 304 MET cc_start: 0.8162 (mtp) cc_final: 0.7765 (mtm) REVERT: B 137 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6284 (tmm160) REVERT: B 202 GLU cc_start: 0.8069 (tt0) cc_final: 0.7697 (tt0) REVERT: B 246 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: B 375 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7296 (mtm180) REVERT: B 405 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.6001 (mm) REVERT: B 503 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4566 (pt) REVERT: B 504 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.5528 (tm-30) REVERT: C 247 ARG cc_start: 0.7417 (mtp85) cc_final: 0.6869 (mtt-85) REVERT: C 251 ASP cc_start: 0.8052 (m-30) cc_final: 0.7254 (m-30) REVERT: D 30 ARG cc_start: 0.7055 (mtp85) cc_final: 0.6702 (mtp85) REVERT: D 49 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8046 (mt) REVERT: D 154 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7790 (mt0) REVERT: D 261 TRP cc_start: 0.8244 (m100) cc_final: 0.8041 (m100) REVERT: E 137 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.5915 (tmm160) REVERT: E 202 GLU cc_start: 0.7999 (tt0) cc_final: 0.7653 (tt0) REVERT: E 246 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: E 375 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7364 (mtm180) REVERT: E 503 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4798 (pt) REVERT: F 247 ARG cc_start: 0.7293 (mtp85) cc_final: 0.6795 (ttt-90) REVERT: F 251 ASP cc_start: 0.8027 (m-30) cc_final: 0.7217 (m-30) REVERT: F 311 ARG cc_start: 0.7680 (ttt-90) cc_final: 0.7477 (ttt180) outliers start: 82 outliers final: 50 residues processed: 251 average time/residue: 0.1521 time to fit residues: 54.8323 Evaluate side-chains 213 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 204 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 91 optimal weight: 0.0060 chunk 98 optimal weight: 20.0000 chunk 8 optimal weight: 0.0000 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN D 202 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.169203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131524 restraints weight = 18559.078| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.26 r_work: 0.3261 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16764 Z= 0.126 Angle : 0.646 8.863 22808 Z= 0.325 Chirality : 0.043 0.172 2564 Planarity : 0.005 0.047 2962 Dihedral : 7.219 58.702 2415 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.16 % Favored : 88.75 % Rotamer: Outliers : 5.16 % Allowed : 16.61 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.18), residues: 2124 helix: 0.82 (0.20), residues: 754 sheet: -1.76 (0.26), residues: 396 loop : -2.72 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 267 TYR 0.013 0.001 TYR A 32 PHE 0.010 0.001 PHE D 262 TRP 0.011 0.001 TRP C 360 HIS 0.013 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00288 (16764) covalent geometry : angle 0.64610 (22808) hydrogen bonds : bond 0.03448 ( 664) hydrogen bonds : angle 4.49106 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 163 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7855 (mt) REVERT: A 87 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7659 (ttp-170) REVERT: A 206 ARG cc_start: 0.8191 (ttp80) cc_final: 0.7618 (ttm170) REVERT: B 137 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.6307 (tmm160) REVERT: B 202 GLU cc_start: 0.8168 (tt0) cc_final: 0.7838 (tt0) REVERT: B 246 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: B 375 ARG cc_start: 0.7634 (mtt180) cc_final: 0.7198 (mtm180) REVERT: B 405 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6036 (mm) REVERT: B 486 ASN cc_start: 0.7394 (t0) cc_final: 0.7183 (t0) REVERT: B 504 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.5690 (tm-30) REVERT: D 30 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6729 (mtp85) REVERT: D 49 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7981 (mt) REVERT: D 154 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7904 (mt0) REVERT: E 137 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6170 (tmm160) REVERT: E 202 GLU cc_start: 0.8096 (tt0) cc_final: 0.7782 (tt0) REVERT: E 246 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: E 375 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7274 (mtm180) REVERT: F 247 ARG cc_start: 0.7378 (mtp85) cc_final: 0.6857 (ttt-90) REVERT: F 251 ASP cc_start: 0.8006 (m-30) cc_final: 0.7174 (m-30) REVERT: F 311 ARG cc_start: 0.7702 (ttt-90) cc_final: 0.7499 (ttt180) outliers start: 87 outliers final: 66 residues processed: 242 average time/residue: 0.1420 time to fit residues: 50.3675 Evaluate side-chains 230 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 156 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 175 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.164298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125983 restraints weight = 18704.532| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.27 r_work: 0.3187 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16764 Z= 0.230 Angle : 0.742 7.201 22808 Z= 0.371 Chirality : 0.047 0.199 2564 Planarity : 0.005 0.048 2962 Dihedral : 7.554 53.250 2410 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.05 % Favored : 87.81 % Rotamer: Outliers : 6.11 % Allowed : 16.37 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.05 (0.18), residues: 2124 helix: 0.63 (0.19), residues: 760 sheet: -1.99 (0.26), residues: 398 loop : -2.80 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.015 0.002 TYR A 32 PHE 0.014 0.002 PHE A 68 TRP 0.014 0.002 TRP C 360 HIS 0.014 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00564 (16764) covalent geometry : angle 0.74173 (22808) hydrogen bonds : bond 0.04393 ( 664) hydrogen bonds : angle 4.65056 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 154 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7879 (mt) REVERT: B 137 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6389 (tmm160) REVERT: B 202 GLU cc_start: 0.8284 (tt0) cc_final: 0.7962 (tt0) REVERT: B 375 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7213 (mtm180) REVERT: B 405 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6006 (mm) REVERT: B 486 ASN cc_start: 0.7617 (t0) cc_final: 0.7248 (t0) REVERT: B 504 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.5695 (tm-30) REVERT: D 30 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6951 (mtp85) REVERT: D 49 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7923 (mt) REVERT: D 154 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7911 (mt0) REVERT: E 137 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6186 (tmm160) REVERT: E 202 GLU cc_start: 0.8287 (tt0) cc_final: 0.7968 (tt0) REVERT: E 375 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7065 (mtm180) outliers start: 103 outliers final: 87 residues processed: 244 average time/residue: 0.1400 time to fit residues: 49.7333 Evaluate side-chains 243 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 150 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 175 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 212 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.166210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.128029 restraints weight = 18540.290| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.27 r_work: 0.3219 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16764 Z= 0.172 Angle : 0.680 6.593 22808 Z= 0.342 Chirality : 0.045 0.176 2564 Planarity : 0.005 0.047 2962 Dihedral : 7.270 53.927 2406 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.39 % Favored : 88.47 % Rotamer: Outliers : 6.23 % Allowed : 16.49 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.18), residues: 2124 helix: 0.82 (0.19), residues: 760 sheet: -1.80 (0.26), residues: 382 loop : -2.75 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.012 0.001 TYR A 32 PHE 0.012 0.001 PHE B 100 TRP 0.012 0.001 TRP F 360 HIS 0.012 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00417 (16764) covalent geometry : angle 0.68033 (22808) hydrogen bonds : bond 0.03875 ( 664) hydrogen bonds : angle 4.53457 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 157 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7854 (mt) REVERT: B 137 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6252 (tmm160) REVERT: B 202 GLU cc_start: 0.8268 (tt0) cc_final: 0.7956 (tt0) REVERT: B 375 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7222 (mtm180) REVERT: B 405 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6077 (mm) REVERT: B 486 ASN cc_start: 0.7594 (t0) cc_final: 0.7208 (t0) REVERT: B 504 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.5728 (tm-30) REVERT: D 49 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7919 (mt) REVERT: D 154 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7966 (mt0) REVERT: E 137 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6214 (tmm160) REVERT: E 202 GLU cc_start: 0.8243 (tt0) cc_final: 0.7937 (tt0) REVERT: E 375 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7052 (mtm180) outliers start: 105 outliers final: 88 residues processed: 252 average time/residue: 0.1375 time to fit residues: 50.6459 Evaluate side-chains 247 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 153 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 53 optimal weight: 0.6980 chunk 81 optimal weight: 0.0010 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.171211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133726 restraints weight = 18398.137| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.25 r_work: 0.3308 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16764 Z= 0.111 Angle : 0.610 8.535 22808 Z= 0.309 Chirality : 0.042 0.150 2564 Planarity : 0.005 0.046 2962 Dihedral : 6.770 55.176 2404 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 4.63 % Allowed : 18.09 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 2124 helix: 1.29 (0.20), residues: 760 sheet: -1.49 (0.28), residues: 368 loop : -2.57 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.010 0.001 TYR E 154 PHE 0.009 0.001 PHE A 103 TRP 0.010 0.001 TRP F 63 HIS 0.009 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00247 (16764) covalent geometry : angle 0.61014 (22808) hydrogen bonds : bond 0.03072 ( 664) hydrogen bonds : angle 4.32620 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 171 time to evaluate : 0.578 Fit side-chains REVERT: A 49 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7792 (mt) REVERT: A 206 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7523 (ttm170) REVERT: A 267 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7404 (mtm110) REVERT: B 137 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6662 (tmm160) REVERT: B 202 GLU cc_start: 0.8153 (tt0) cc_final: 0.7853 (tt0) REVERT: B 246 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: B 375 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7227 (mtm180) REVERT: B 405 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5856 (mm) REVERT: B 504 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.5653 (tm-30) REVERT: C 52 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7015 (tm) REVERT: C 247 ARG cc_start: 0.7287 (mtt-85) cc_final: 0.6714 (mtt-85) REVERT: C 251 ASP cc_start: 0.7894 (m-30) cc_final: 0.7289 (m-30) REVERT: C 300 TYR cc_start: 0.8241 (m-80) cc_final: 0.7972 (m-80) REVERT: C 395 LEU cc_start: 0.7514 (mt) cc_final: 0.7314 (mt) REVERT: D 30 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6884 (mtp85) REVERT: D 49 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7958 (mt) REVERT: D 154 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7746 (mt0) REVERT: E 137 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6596 (tmm160) REVERT: E 202 GLU cc_start: 0.8129 (tt0) cc_final: 0.7802 (tt0) REVERT: E 246 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: E 286 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6715 (mm110) REVERT: E 375 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7061 (mtm180) REVERT: F 52 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7064 (tm) REVERT: F 251 ASP cc_start: 0.7958 (m-30) cc_final: 0.7167 (m-30) outliers start: 78 outliers final: 57 residues processed: 241 average time/residue: 0.1530 time to fit residues: 52.4805 Evaluate side-chains 229 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 134 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 chunk 165 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.170221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132594 restraints weight = 18446.258| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.26 r_work: 0.3289 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16764 Z= 0.123 Angle : 0.622 6.838 22808 Z= 0.313 Chirality : 0.043 0.172 2564 Planarity : 0.005 0.046 2962 Dihedral : 6.706 57.030 2401 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 5.34 % Allowed : 17.85 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.19), residues: 2124 helix: 1.38 (0.20), residues: 760 sheet: -1.44 (0.28), residues: 362 loop : -2.55 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.013 0.001 TYR B 154 PHE 0.009 0.001 PHE E 396 TRP 0.012 0.001 TRP C 360 HIS 0.009 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00281 (16764) covalent geometry : angle 0.62150 (22808) hydrogen bonds : bond 0.03244 ( 664) hydrogen bonds : angle 4.30298 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 167 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 206 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7506 (ttm170) REVERT: A 267 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7388 (mtm110) REVERT: B 137 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6631 (tmm160) REVERT: B 202 GLU cc_start: 0.8173 (tt0) cc_final: 0.7880 (tt0) REVERT: B 246 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: B 375 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7231 (mtm180) REVERT: B 405 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5850 (mm) REVERT: B 504 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.5760 (tm-30) REVERT: C 247 ARG cc_start: 0.7493 (mtt-85) cc_final: 0.7237 (mtp85) REVERT: C 395 LEU cc_start: 0.7548 (mt) cc_final: 0.7335 (mt) REVERT: D 30 ARG cc_start: 0.7095 (mtp85) cc_final: 0.6849 (mtp85) REVERT: D 49 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7879 (mt) REVERT: D 154 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7824 (mt0) REVERT: E 105 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7539 (t80) REVERT: E 137 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6573 (tmm160) REVERT: E 202 GLU cc_start: 0.8195 (tt0) cc_final: 0.7900 (tt0) REVERT: E 246 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: E 286 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6767 (mm110) REVERT: E 375 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7071 (mtm180) outliers start: 90 outliers final: 73 residues processed: 251 average time/residue: 0.1514 time to fit residues: 54.2558 Evaluate side-chains 242 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 159 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 162 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.167970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129979 restraints weight = 18490.173| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.26 r_work: 0.3259 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16764 Z= 0.164 Angle : 0.668 11.611 22808 Z= 0.333 Chirality : 0.044 0.223 2564 Planarity : 0.005 0.046 2962 Dihedral : 6.741 54.795 2396 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.06 % Favored : 88.84 % Rotamer: Outliers : 5.93 % Allowed : 17.44 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 2124 helix: 1.32 (0.20), residues: 760 sheet: -1.53 (0.28), residues: 364 loop : -2.58 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.014 0.001 TYR E 154 PHE 0.010 0.001 PHE E 100 TRP 0.013 0.001 TRP F 360 HIS 0.010 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00395 (16764) covalent geometry : angle 0.66758 (22808) hydrogen bonds : bond 0.03580 ( 664) hydrogen bonds : angle 4.36657 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 159 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7647 (mt) REVERT: A 206 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7612 (ttm170) REVERT: A 267 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7328 (mtm110) REVERT: B 105 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7539 (t80) REVERT: B 137 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6510 (tmm160) REVERT: B 202 GLU cc_start: 0.8287 (tt0) cc_final: 0.8017 (tt0) REVERT: B 246 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: B 286 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6641 (mm110) REVERT: B 375 ARG cc_start: 0.7652 (mtt180) cc_final: 0.7216 (mtm180) REVERT: B 405 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5808 (mm) REVERT: B 504 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.5746 (tm-30) REVERT: C 395 LEU cc_start: 0.7554 (mt) cc_final: 0.7348 (mt) REVERT: D 30 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6768 (mtp85) REVERT: D 49 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7836 (mt) REVERT: D 154 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7880 (mt0) REVERT: E 105 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7614 (t80) REVERT: E 137 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6392 (tmm160) REVERT: E 202 GLU cc_start: 0.8223 (tt0) cc_final: 0.7930 (tt0) REVERT: E 246 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: E 286 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6781 (mm110) REVERT: E 375 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7068 (mtm180) outliers start: 100 outliers final: 84 residues processed: 250 average time/residue: 0.1451 time to fit residues: 52.1644 Evaluate side-chains 254 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 158 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 360 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 431 ASN Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 151 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 203 optimal weight: 0.0570 chunk 211 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.168523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130354 restraints weight = 18456.695| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.27 r_work: 0.3246 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16764 Z= 0.151 Angle : 0.662 11.460 22808 Z= 0.331 Chirality : 0.044 0.237 2564 Planarity : 0.005 0.046 2962 Dihedral : 6.798 58.887 2396 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.97 % Favored : 88.89 % Rotamer: Outliers : 5.87 % Allowed : 17.38 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.19), residues: 2124 helix: 1.31 (0.20), residues: 760 sheet: -1.53 (0.29), residues: 348 loop : -2.55 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.016 0.001 TYR B 154 PHE 0.009 0.001 PHE E 396 TRP 0.013 0.001 TRP F 360 HIS 0.010 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00361 (16764) covalent geometry : angle 0.66214 (22808) hydrogen bonds : bond 0.03551 ( 664) hydrogen bonds : angle 4.37369 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 160 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7656 (mt) REVERT: A 206 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7627 (ttm170) REVERT: A 267 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7300 (mtm110) REVERT: B 105 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7540 (t80) REVERT: B 137 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6355 (tmm160) REVERT: B 202 GLU cc_start: 0.8276 (tt0) cc_final: 0.8002 (tt0) REVERT: B 286 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6632 (mm110) REVERT: B 375 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7134 (mtm180) REVERT: B 405 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5838 (mm) REVERT: B 417 ARG cc_start: 0.7830 (tpp80) cc_final: 0.7593 (tpp80) REVERT: B 504 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.5690 (tm-30) REVERT: C 299 ARG cc_start: 0.7187 (mtt-85) cc_final: 0.6899 (mtt180) REVERT: C 395 LEU cc_start: 0.7565 (mt) cc_final: 0.7364 (mt) REVERT: D 49 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7847 (mt) REVERT: D 154 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7886 (mt0) REVERT: E 105 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7558 (t80) REVERT: E 137 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6335 (tmm160) REVERT: E 202 GLU cc_start: 0.8221 (tt0) cc_final: 0.7926 (tt0) REVERT: E 286 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6790 (mm110) REVERT: E 375 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7119 (mtm180) REVERT: F 247 ARG cc_start: 0.7550 (mtt-85) cc_final: 0.6709 (mtp85) REVERT: F 251 ASP cc_start: 0.8110 (m-30) cc_final: 0.7282 (m-30) outliers start: 99 outliers final: 87 residues processed: 250 average time/residue: 0.1536 time to fit residues: 55.0173 Evaluate side-chains 255 residues out of total 1686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 158 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 431 ASN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 105 PHE Chi-restraints excluded: chain E residue 136 SER Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 286 GLN Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain E residue 507 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 292 LEU Chi-restraints excluded: chain F residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 21 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 133 optimal weight: 0.4980 chunk 137 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.165369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127821 restraints weight = 18573.030| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.19 r_work: 0.3239 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16764 Z= 0.199 Angle : 0.714 10.766 22808 Z= 0.356 Chirality : 0.046 0.220 2564 Planarity : 0.005 0.046 2962 Dihedral : 7.080 59.890 2396 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.53 % Favored : 88.32 % Rotamer: Outliers : 6.23 % Allowed : 17.08 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2124 helix: 1.20 (0.20), residues: 748 sheet: -1.68 (0.28), residues: 348 loop : -2.67 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 299 TYR 0.018 0.002 TYR E 154 PHE 0.012 0.002 PHE A 68 TRP 0.013 0.002 TRP F 360 HIS 0.011 0.001 HIS F 172 Details of bonding type rmsd covalent geometry : bond 0.00485 (16764) covalent geometry : angle 0.71386 (22808) hydrogen bonds : bond 0.04009 ( 664) hydrogen bonds : angle 4.48105 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3729.92 seconds wall clock time: 64 minutes 29.18 seconds (3869.18 seconds total)