Starting phenix.real_space_refine on Thu Mar 5 05:32:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6n_32330/03_2026/7w6n_32330.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6n_32330/03_2026/7w6n_32330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w6n_32330/03_2026/7w6n_32330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6n_32330/03_2026/7w6n_32330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w6n_32330/03_2026/7w6n_32330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6n_32330/03_2026/7w6n_32330.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 132 5.16 5 C 12748 2.51 5 N 3276 2.21 5 O 3564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 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: 19720 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1474 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 174} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3456 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 2 Restraints were copied for chains: C, E, G, D, F, H Time building chain proxies: 3.13, per 1000 atoms: 0.16 Number of scatterers: 19720 At special positions: 0 Unit cell: (161.226, 161.226, 126.75, 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 132 16.00 O 3564 8.00 N 3276 7.00 C 12748 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: 1.49 Conformation dependent library (CDL) restraints added in 763.4 milliseconds 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 8 sheets defined 67.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.407A pdb=" N GLN A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.414A pdb=" N TYR A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN A 107 " --> pdb=" O HIS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 4.133A pdb=" N ALA A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.802A pdb=" N ARG A 139 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.631A pdb=" N ILE A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 189 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.502A pdb=" N ALA B 6 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 7 " --> pdb=" O GLY B 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 7' Processing helix chain 'B' and resid 8 through 17 removed outlier: 3.949A pdb=" N ILE B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.839A pdb=" N PHE B 73 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 74 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 75' Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.547A pdb=" N GLU B 174 " --> pdb=" O TRP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 222 through 247 removed outlier: 3.696A pdb=" N LEU B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 276 Proline residue: B 269 - end of helix removed outlier: 3.774A pdb=" N GLY B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 removed outlier: 3.921A pdb=" N PHE B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 removed outlier: 3.738A pdb=" N PHE B 298 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 302 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 removed outlier: 3.893A pdb=" N ARG B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU B 321 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.661A pdb=" N THR B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 396 removed outlier: 3.644A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 426 removed outlier: 4.350A pdb=" N VAL B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.804A pdb=" N LEU B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 4.407A pdb=" N GLN C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 93 Processing helix chain 'C' and resid 98 through 110 removed outlier: 4.413A pdb=" N TYR C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 removed outlier: 4.133A pdb=" N ALA C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.802A pdb=" N ARG C 139 " --> pdb=" O HIS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.632A pdb=" N ILE C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 170 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE C 189 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.502A pdb=" N ALA D 6 " --> pdb=" O ALA D 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 7 " --> pdb=" O GLY D 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3 through 7' Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.950A pdb=" N ILE D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.838A pdb=" N PHE D 73 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 74 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 75' Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 167 through 174 removed outlier: 3.549A pdb=" N GLU D 174 " --> pdb=" O TRP D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE D 191 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 222 through 247 removed outlier: 3.696A pdb=" N LEU D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 276 Proline residue: D 269 - end of helix removed outlier: 3.774A pdb=" N GLY D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 291 removed outlier: 3.921A pdb=" N PHE D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 302 removed outlier: 3.738A pdb=" N PHE D 298 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 302 " --> pdb=" O LYS D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 3.892A pdb=" N ARG D 308 " --> pdb=" O SER D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU D 321 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 366 removed outlier: 3.661A pdb=" N THR D 361 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 396 removed outlier: 3.646A pdb=" N LEU D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 426 removed outlier: 4.350A pdb=" N VAL D 401 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.807A pdb=" N LEU D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 480 " --> pdb=" O HIS D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 removed outlier: 4.406A pdb=" N GLN E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 93 Processing helix chain 'E' and resid 98 through 110 removed outlier: 4.414A pdb=" N TYR E 104 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 105 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN E 107 " --> pdb=" O HIS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 132 removed outlier: 4.132A pdb=" N ALA E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 146 removed outlier: 3.803A pdb=" N ARG E 139 " --> pdb=" O HIS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.631A pdb=" N ILE E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY E 170 " --> pdb=" O TYR E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL E 186 " --> pdb=" O PRO E 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE E 189 " --> pdb=" O HIS E 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.502A pdb=" N ALA F 6 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 7 " --> pdb=" O GLY F 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3 through 7' Processing helix chain 'F' and resid 8 through 17 removed outlier: 3.949A pdb=" N ILE F 17 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'F' and resid 70 through 75 removed outlier: 3.839A pdb=" N PHE F 73 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE F 74 " --> pdb=" O LYS F 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE F 75 " --> pdb=" O GLU F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 70 through 75' Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 129 through 132 Processing helix chain 'F' and resid 133 through 148 Processing helix chain 'F' and resid 167 through 174 removed outlier: 3.549A pdb=" N GLU F 174 " --> pdb=" O TRP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE F 191 " --> pdb=" O TYR F 187 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE F 192 " --> pdb=" O VAL F 188 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE F 193 " --> pdb=" O THR F 189 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 222 through 247 removed outlier: 3.696A pdb=" N LEU F 243 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 276 Proline residue: F 269 - end of helix removed outlier: 3.774A pdb=" N GLY F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 291 removed outlier: 3.921A pdb=" N PHE F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 302 removed outlier: 3.738A pdb=" N PHE F 298 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG F 302 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 317 removed outlier: 3.891A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU F 321 " --> pdb=" O CYS F 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE F 323 " --> pdb=" O SER F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.660A pdb=" N THR F 361 " --> pdb=" O SER F 357 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 366 " --> pdb=" O ILE F 362 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 396 removed outlier: 3.646A pdb=" N LEU F 389 " --> pdb=" O SER F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 426 removed outlier: 4.351A pdb=" N VAL F 401 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.806A pdb=" N LEU F 479 " --> pdb=" O GLN F 475 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 480 " --> pdb=" O HIS F 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 61 through 75 removed outlier: 3.923A pdb=" N LEU G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 89 removed outlier: 4.407A pdb=" N GLN G 87 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 93 Processing helix chain 'G' and resid 98 through 110 removed outlier: 4.413A pdb=" N TYR G 104 " --> pdb=" O THR G 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU G 105 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 132 removed outlier: 4.132A pdb=" N ALA G 125 " --> pdb=" O ASP G 121 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 146 removed outlier: 3.802A pdb=" N ARG G 139 " --> pdb=" O HIS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.631A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA G 164 " --> pdb=" O ASP G 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY G 170 " --> pdb=" O TYR G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.525A pdb=" N VAL G 186 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE G 189 " --> pdb=" O HIS G 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE G 190 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS G 192 " --> pdb=" O VAL G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'G' and resid 213 through 220 Processing helix chain 'H' and resid 3 through 7 removed outlier: 3.501A pdb=" N ALA H 6 " --> pdb=" O ALA H 3 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA H 7 " --> pdb=" O GLY H 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 7' Processing helix chain 'H' and resid 8 through 17 removed outlier: 3.950A pdb=" N ILE H 17 " --> pdb=" O ARG H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 59 Processing helix chain 'H' and resid 70 through 75 removed outlier: 3.840A pdb=" N PHE H 73 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE H 74 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE H 75 " --> pdb=" O GLU H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 70 through 75' Processing helix chain 'H' and resid 90 through 100 Processing helix chain 'H' and resid 110 through 122 Processing helix chain 'H' and resid 124 through 128 Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.549A pdb=" N GLU H 174 " --> pdb=" O TRP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 203 removed outlier: 3.655A pdb=" N LEU H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE H 191 " --> pdb=" O TYR H 187 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE H 192 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE H 193 " --> pdb=" O THR H 189 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA H 194 " --> pdb=" O GLY H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 222 through 247 removed outlier: 3.695A pdb=" N LEU H 243 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 276 Proline residue: H 269 - end of helix removed outlier: 3.774A pdb=" N GLY H 273 " --> pdb=" O PRO H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 291 removed outlier: 3.922A pdb=" N PHE H 286 " --> pdb=" O VAL H 282 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL H 287 " --> pdb=" O SER H 283 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N THR H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 302 removed outlier: 3.739A pdb=" N PHE H 298 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 317 removed outlier: 3.893A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 344 removed outlier: 3.604A pdb=" N LEU H 321 " --> pdb=" O CYS H 317 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE H 323 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 366 removed outlier: 3.661A pdb=" N THR H 361 " --> pdb=" O SER H 357 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR H 366 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 396 removed outlier: 3.646A pdb=" N LEU H 389 " --> pdb=" O SER H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 426 removed outlier: 4.350A pdb=" N VAL H 401 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL H 403 " --> pdb=" O VAL H 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG H 426 " --> pdb=" O GLN H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 484 removed outlier: 3.804A pdb=" N LEU H 479 " --> pdb=" O GLN H 475 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU H 480 " --> pdb=" O HIS H 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL A 201 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL C 201 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 49 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL E 201 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 49 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.663A pdb=" N VAL G 201 " --> pdb=" O ILE G 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 49 through 54 965 hydrogen bonds defined for protein. 2739 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: 2.97 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5579 1.33 - 1.45: 3673 1.45 - 1.57: 10740 1.57 - 1.69: 0 1.69 - 1.80: 208 Bond restraints: 20200 Sorted by residual: bond pdb=" CB VAL D 46 " pdb=" CG2 VAL D 46 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 bond pdb=" CB VAL F 46 " pdb=" CG2 VAL F 46 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.22e+00 bond pdb=" CB VAL H 46 " pdb=" CG2 VAL H 46 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.15e+00 bond pdb=" CB VAL B 46 " pdb=" CG2 VAL B 46 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 4.98e+00 bond pdb=" CE2 PHE H 91 " pdb=" CZ PHE H 91 " ideal model delta sigma weight residual 1.382 1.323 0.059 3.00e-02 1.11e+03 3.84e+00 ... (remaining 20195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 26360 2.11 - 4.23: 846 4.23 - 6.34: 97 6.34 - 8.45: 17 8.45 - 10.56: 8 Bond angle restraints: 27328 Sorted by residual: angle pdb=" C PHE A 223 " pdb=" N GLN A 224 " pdb=" CA GLN A 224 " ideal model delta sigma weight residual 122.55 112.73 9.82 2.03e+00 2.43e-01 2.34e+01 angle pdb=" C PHE E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta sigma weight residual 122.55 112.76 9.79 2.03e+00 2.43e-01 2.33e+01 angle pdb=" C PHE C 223 " pdb=" N GLN C 224 " pdb=" CA GLN C 224 " ideal model delta sigma weight residual 122.55 112.76 9.79 2.03e+00 2.43e-01 2.33e+01 angle pdb=" C PHE G 223 " pdb=" N GLN G 224 " pdb=" CA GLN G 224 " ideal model delta sigma weight residual 122.55 112.79 9.76 2.03e+00 2.43e-01 2.31e+01 angle pdb=" C GLY C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta sigma weight residual 121.97 129.38 -7.41 1.80e+00 3.09e-01 1.69e+01 ... (remaining 27323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 10068 14.91 - 29.82: 1481 29.82 - 44.74: 327 44.74 - 59.65: 88 59.65 - 74.56: 16 Dihedral angle restraints: 11980 sinusoidal: 4816 harmonic: 7164 Sorted by residual: dihedral pdb=" CA GLY C 78 " pdb=" C GLY C 78 " pdb=" N VAL C 79 " pdb=" CA VAL C 79 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLY A 78 " pdb=" C GLY A 78 " pdb=" N VAL A 79 " pdb=" CA VAL A 79 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLY E 78 " pdb=" C GLY E 78 " pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta harmonic sigma weight residual 180.00 151.76 28.24 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 11977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1590 0.036 - 0.072: 901 0.072 - 0.108: 411 0.108 - 0.144: 94 0.144 - 0.180: 16 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CG LEU B 44 " pdb=" CB LEU B 44 " pdb=" CD1 LEU B 44 " pdb=" CD2 LEU B 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CG LEU H 44 " pdb=" CB LEU H 44 " pdb=" CD1 LEU H 44 " pdb=" CD2 LEU H 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CG LEU F 44 " pdb=" CB LEU F 44 " pdb=" CD1 LEU F 44 " pdb=" CD2 LEU F 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3009 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 75 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO C 76 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 75 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO E 76 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 87 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO D 88 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.035 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 390 2.62 - 3.19: 20213 3.19 - 3.76: 30264 3.76 - 4.33: 41728 4.33 - 4.90: 67003 Nonbonded interactions: 159598 Sorted by model distance: nonbonded pdb=" O THR B 64 " pdb=" OG SER B 68 " model vdw 2.045 3.040 nonbonded pdb=" O THR F 64 " pdb=" OG SER F 68 " model vdw 2.046 3.040 nonbonded pdb=" O THR H 64 " pdb=" OG SER H 68 " model vdw 2.046 3.040 nonbonded pdb=" O THR D 64 " pdb=" OG SER D 68 " model vdw 2.047 3.040 nonbonded pdb=" O HIS F 104 " pdb=" OH TYR F 114 " model vdw 2.096 3.040 ... (remaining 159593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.480 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.011 0.075 20200 Z= 0.466 Angle : 0.898 10.564 27328 Z= 0.502 Chirality : 0.051 0.180 3012 Planarity : 0.006 0.064 3468 Dihedral : 14.870 74.560 7356 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 0.37 % Allowed : 11.89 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.14), residues: 2404 helix: -2.40 (0.11), residues: 1436 sheet: -3.92 (0.66), residues: 40 loop : -3.31 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 183 TYR 0.022 0.002 TYR H 270 PHE 0.024 0.003 PHE A 71 TRP 0.009 0.003 TRP B 359 HIS 0.009 0.002 HIS B 481 Details of bonding type rmsd covalent geometry : bond 0.01097 (20200) covalent geometry : angle 0.89802 (27328) hydrogen bonds : bond 0.17084 ( 965) hydrogen bonds : angle 7.07859 ( 2739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 460 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8221 (mtt-85) REVERT: A 204 ASP cc_start: 0.7818 (t0) cc_final: 0.7528 (t0) REVERT: B 270 TYR cc_start: 0.7198 (t80) cc_final: 0.6994 (t80) REVERT: B 292 PHE cc_start: 0.8975 (m-80) cc_final: 0.8771 (m-80) REVERT: B 299 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8471 (tttp) REVERT: B 328 LEU cc_start: 0.7685 (mt) cc_final: 0.7447 (mt) REVERT: C 183 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.8222 (mtt-85) REVERT: C 204 ASP cc_start: 0.7823 (t0) cc_final: 0.7533 (t0) REVERT: D 270 TYR cc_start: 0.7195 (t80) cc_final: 0.6995 (t80) REVERT: D 292 PHE cc_start: 0.8974 (m-80) cc_final: 0.8772 (m-80) REVERT: D 299 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8472 (tttp) REVERT: D 328 LEU cc_start: 0.7682 (mt) cc_final: 0.7443 (mt) REVERT: E 183 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8210 (mtt-85) REVERT: E 204 ASP cc_start: 0.7832 (t0) cc_final: 0.7538 (t0) REVERT: F 270 TYR cc_start: 0.7200 (t80) cc_final: 0.6995 (t80) REVERT: F 292 PHE cc_start: 0.8977 (m-80) cc_final: 0.8771 (m-80) REVERT: F 299 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8471 (tttp) REVERT: F 328 LEU cc_start: 0.7687 (mt) cc_final: 0.7447 (mt) REVERT: G 183 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8212 (mtt-85) REVERT: G 204 ASP cc_start: 0.7827 (t0) cc_final: 0.7535 (t0) REVERT: H 270 TYR cc_start: 0.7199 (t80) cc_final: 0.6995 (t80) REVERT: H 292 PHE cc_start: 0.8974 (m-80) cc_final: 0.8769 (m-80) REVERT: H 299 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8471 (tttp) REVERT: H 328 LEU cc_start: 0.7639 (mt) cc_final: 0.7399 (mt) outliers start: 8 outliers final: 0 residues processed: 468 average time/residue: 0.1665 time to fit residues: 113.4231 Evaluate side-chains 378 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 87 GLN A 185 HIS B 24 ASN B 177 HIS B 476 HIS C 58 ASN C 87 GLN C 185 HIS D 24 ASN D 177 HIS D 476 HIS E 87 GLN E 185 HIS F 24 ASN F 177 HIS F 476 HIS G 87 GLN G 185 HIS H 24 ASN H 177 HIS H 476 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115863 restraints weight = 32208.122| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.72 r_work: 0.3309 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20200 Z= 0.212 Angle : 0.693 9.058 27328 Z= 0.362 Chirality : 0.044 0.160 3012 Planarity : 0.006 0.062 3468 Dihedral : 5.508 34.615 2684 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.52 % Allowed : 17.02 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.82 (0.16), residues: 2404 helix: -1.32 (0.12), residues: 1512 sheet: None (None), residues: 0 loop : -2.72 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 166 TYR 0.015 0.001 TYR H 270 PHE 0.016 0.002 PHE E 71 TRP 0.009 0.002 TRP D 359 HIS 0.004 0.001 HIS B 481 Details of bonding type rmsd covalent geometry : bond 0.00509 (20200) covalent geometry : angle 0.69347 (27328) hydrogen bonds : bond 0.04615 ( 965) hydrogen bonds : angle 5.23803 ( 2739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 459 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8944 (t0) cc_final: 0.8458 (t0) REVERT: A 104 TYR cc_start: 0.8375 (m-80) cc_final: 0.8138 (m-80) REVERT: A 107 ASN cc_start: 0.7891 (t0) cc_final: 0.7518 (t0) REVERT: A 160 ASP cc_start: 0.7598 (t0) cc_final: 0.7243 (t0) REVERT: A 183 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8188 (mtm180) REVERT: A 204 ASP cc_start: 0.8216 (t0) cc_final: 0.7786 (t0) REVERT: B 271 TYR cc_start: 0.7824 (m-10) cc_final: 0.7607 (m-10) REVERT: B 292 PHE cc_start: 0.9063 (m-80) cc_final: 0.8835 (m-80) REVERT: B 299 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8304 (tttp) REVERT: B 405 ASN cc_start: 0.9179 (m110) cc_final: 0.8907 (m110) REVERT: B 414 GLN cc_start: 0.8025 (tp40) cc_final: 0.7532 (tp40) REVERT: B 418 LYS cc_start: 0.8912 (tptp) cc_final: 0.8496 (ptpp) REVERT: C 73 ASN cc_start: 0.8947 (t0) cc_final: 0.8458 (t0) REVERT: C 104 TYR cc_start: 0.8380 (m-80) cc_final: 0.8141 (m-80) REVERT: C 107 ASN cc_start: 0.7894 (t0) cc_final: 0.7521 (t0) REVERT: C 160 ASP cc_start: 0.7596 (t0) cc_final: 0.7245 (t0) REVERT: C 183 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8187 (mtm180) REVERT: C 204 ASP cc_start: 0.8210 (t0) cc_final: 0.7777 (t0) REVERT: D 271 TYR cc_start: 0.7822 (m-10) cc_final: 0.7605 (m-10) REVERT: D 292 PHE cc_start: 0.9061 (m-80) cc_final: 0.8834 (m-80) REVERT: D 299 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8300 (tttp) REVERT: D 405 ASN cc_start: 0.9182 (m110) cc_final: 0.8909 (m110) REVERT: D 414 GLN cc_start: 0.8035 (tp40) cc_final: 0.7540 (tp40) REVERT: D 418 LYS cc_start: 0.8907 (tptp) cc_final: 0.8492 (ptpp) REVERT: E 73 ASN cc_start: 0.8938 (t0) cc_final: 0.8450 (t0) REVERT: E 104 TYR cc_start: 0.8384 (m-80) cc_final: 0.8147 (m-80) REVERT: E 107 ASN cc_start: 0.7897 (t0) cc_final: 0.7525 (t0) REVERT: E 160 ASP cc_start: 0.7618 (t0) cc_final: 0.7263 (t0) REVERT: E 183 ARG cc_start: 0.8926 (mmm-85) cc_final: 0.8186 (mtm180) REVERT: E 204 ASP cc_start: 0.8219 (t0) cc_final: 0.7788 (t0) REVERT: F 271 TYR cc_start: 0.7825 (m-10) cc_final: 0.7608 (m-10) REVERT: F 292 PHE cc_start: 0.9063 (m-80) cc_final: 0.8832 (m-80) REVERT: F 299 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8303 (tttp) REVERT: F 405 ASN cc_start: 0.9175 (m110) cc_final: 0.8904 (m110) REVERT: F 414 GLN cc_start: 0.8025 (tp40) cc_final: 0.7533 (tp40) REVERT: F 418 LYS cc_start: 0.8906 (tptp) cc_final: 0.8493 (ptpp) REVERT: G 73 ASN cc_start: 0.8942 (t0) cc_final: 0.8455 (t0) REVERT: G 104 TYR cc_start: 0.8383 (m-80) cc_final: 0.8146 (m-80) REVERT: G 107 ASN cc_start: 0.7890 (t0) cc_final: 0.7512 (t0) REVERT: G 160 ASP cc_start: 0.7609 (t0) cc_final: 0.7254 (t0) REVERT: G 183 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8187 (mtm180) REVERT: G 204 ASP cc_start: 0.8224 (t0) cc_final: 0.7789 (t0) REVERT: H 271 TYR cc_start: 0.7823 (m-10) cc_final: 0.7603 (m-10) REVERT: H 292 PHE cc_start: 0.9060 (m-80) cc_final: 0.8831 (m-80) REVERT: H 299 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8298 (tttp) REVERT: H 405 ASN cc_start: 0.9179 (m110) cc_final: 0.8911 (m110) REVERT: H 414 GLN cc_start: 0.8029 (tp40) cc_final: 0.7536 (tp40) REVERT: H 418 LYS cc_start: 0.8911 (tptp) cc_final: 0.8499 (ptpp) outliers start: 54 outliers final: 22 residues processed: 495 average time/residue: 0.1624 time to fit residues: 119.1533 Evaluate side-chains 418 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 396 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 366 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 103 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 ASN H 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117655 restraints weight = 32344.429| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.57 r_work: 0.3369 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20200 Z= 0.130 Angle : 0.630 9.205 27328 Z= 0.323 Chirality : 0.041 0.148 3012 Planarity : 0.005 0.052 3468 Dihedral : 5.029 37.515 2684 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.47 % Allowed : 18.28 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.92 (0.16), residues: 2404 helix: -0.67 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -2.22 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 171 TYR 0.010 0.001 TYR D 186 PHE 0.020 0.002 PHE G 189 TRP 0.008 0.001 TRP D 359 HIS 0.002 0.000 HIS B 481 Details of bonding type rmsd covalent geometry : bond 0.00295 (20200) covalent geometry : angle 0.63035 (27328) hydrogen bonds : bond 0.03643 ( 965) hydrogen bonds : angle 4.74488 ( 2739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 466 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8878 (t0) cc_final: 0.8401 (t0) REVERT: A 104 TYR cc_start: 0.8278 (m-80) cc_final: 0.8008 (m-80) REVERT: A 107 ASN cc_start: 0.7633 (t0) cc_final: 0.7286 (t0) REVERT: A 140 TRP cc_start: 0.8646 (t60) cc_final: 0.8224 (t60) REVERT: A 159 MET cc_start: 0.7415 (ttm) cc_final: 0.6869 (ttp) REVERT: A 160 ASP cc_start: 0.7519 (t0) cc_final: 0.7206 (t0) REVERT: A 189 PHE cc_start: 0.8120 (t80) cc_final: 0.7810 (t80) REVERT: A 204 ASP cc_start: 0.8265 (t0) cc_final: 0.7760 (t0) REVERT: B 193 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7601 (pp) REVERT: B 299 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8214 (tttp) REVERT: B 300 PHE cc_start: 0.8290 (m-80) cc_final: 0.7428 (m-80) REVERT: B 401 VAL cc_start: 0.9329 (m) cc_final: 0.9057 (m) REVERT: B 405 ASN cc_start: 0.9204 (m110) cc_final: 0.8911 (m110) REVERT: C 73 ASN cc_start: 0.8870 (t0) cc_final: 0.8390 (t0) REVERT: C 104 TYR cc_start: 0.8281 (m-80) cc_final: 0.8009 (m-80) REVERT: C 107 ASN cc_start: 0.7636 (t0) cc_final: 0.7284 (t0) REVERT: C 140 TRP cc_start: 0.8640 (t60) cc_final: 0.8302 (t60) REVERT: C 160 ASP cc_start: 0.7517 (t0) cc_final: 0.7203 (t0) REVERT: C 183 ARG cc_start: 0.8963 (mmm-85) cc_final: 0.8206 (mtm180) REVERT: C 189 PHE cc_start: 0.8122 (t80) cc_final: 0.7811 (t80) REVERT: C 204 ASP cc_start: 0.8225 (t0) cc_final: 0.7719 (t0) REVERT: D 193 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7591 (pp) REVERT: D 299 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8209 (tttp) REVERT: D 300 PHE cc_start: 0.8285 (m-80) cc_final: 0.7420 (m-80) REVERT: D 401 VAL cc_start: 0.9324 (m) cc_final: 0.9048 (m) REVERT: D 405 ASN cc_start: 0.9206 (m110) cc_final: 0.8912 (m110) REVERT: E 73 ASN cc_start: 0.8875 (t0) cc_final: 0.8395 (t0) REVERT: E 104 TYR cc_start: 0.8286 (m-80) cc_final: 0.8012 (m-80) REVERT: E 107 ASN cc_start: 0.7634 (t0) cc_final: 0.7287 (t0) REVERT: E 140 TRP cc_start: 0.8648 (t60) cc_final: 0.8239 (t60) REVERT: E 159 MET cc_start: 0.7437 (ttm) cc_final: 0.6898 (ttp) REVERT: E 160 ASP cc_start: 0.7530 (t0) cc_final: 0.7215 (t0) REVERT: E 189 PHE cc_start: 0.8120 (t80) cc_final: 0.7807 (t80) REVERT: E 204 ASP cc_start: 0.8237 (t0) cc_final: 0.7732 (t0) REVERT: F 193 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7603 (pp) REVERT: F 299 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8211 (tttp) REVERT: F 300 PHE cc_start: 0.8286 (m-80) cc_final: 0.7414 (m-80) REVERT: F 401 VAL cc_start: 0.9323 (m) cc_final: 0.9053 (m) REVERT: F 405 ASN cc_start: 0.9207 (m110) cc_final: 0.8913 (m110) REVERT: G 73 ASN cc_start: 0.8870 (t0) cc_final: 0.8394 (t0) REVERT: G 104 TYR cc_start: 0.8284 (m-80) cc_final: 0.8014 (m-80) REVERT: G 107 ASN cc_start: 0.7621 (t0) cc_final: 0.7277 (t0) REVERT: G 140 TRP cc_start: 0.8652 (t60) cc_final: 0.8240 (t60) REVERT: G 159 MET cc_start: 0.7434 (ttm) cc_final: 0.6906 (ttp) REVERT: G 160 ASP cc_start: 0.7523 (t0) cc_final: 0.7207 (t0) REVERT: G 189 PHE cc_start: 0.8127 (t80) cc_final: 0.7813 (t80) REVERT: G 204 ASP cc_start: 0.8231 (t0) cc_final: 0.7726 (t0) REVERT: H 193 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7604 (pp) REVERT: H 299 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8215 (tttp) REVERT: H 300 PHE cc_start: 0.8290 (m-80) cc_final: 0.7425 (m-80) outliers start: 53 outliers final: 18 residues processed: 510 average time/residue: 0.1492 time to fit residues: 115.6793 Evaluate side-chains 444 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 422 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 215 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 135 HIS A 196 ASN C 58 ASN C 135 HIS C 196 ASN E 135 HIS E 196 ASN G 135 HIS G 196 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.169518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125445 restraints weight = 32648.446| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.60 r_work: 0.3439 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20200 Z= 0.132 Angle : 0.624 9.269 27328 Z= 0.316 Chirality : 0.041 0.138 3012 Planarity : 0.005 0.054 3468 Dihedral : 4.811 36.294 2684 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.68 % Allowed : 19.82 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.49 (0.17), residues: 2404 helix: -0.34 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 183 TYR 0.010 0.001 TYR H 271 PHE 0.022 0.002 PHE A 142 TRP 0.008 0.001 TRP D 359 HIS 0.002 0.000 HIS B 481 Details of bonding type rmsd covalent geometry : bond 0.00310 (20200) covalent geometry : angle 0.62427 (27328) hydrogen bonds : bond 0.03522 ( 965) hydrogen bonds : angle 4.61214 ( 2739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 475 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8890 (t0) cc_final: 0.8411 (t0) REVERT: A 104 TYR cc_start: 0.8242 (m-80) cc_final: 0.7841 (m-80) REVERT: A 107 ASN cc_start: 0.7504 (t0) cc_final: 0.7140 (t0) REVERT: A 140 TRP cc_start: 0.8619 (t60) cc_final: 0.8206 (t60) REVERT: A 160 ASP cc_start: 0.7460 (t0) cc_final: 0.7253 (t0) REVERT: A 189 PHE cc_start: 0.7959 (t80) cc_final: 0.7753 (t80) REVERT: A 204 ASP cc_start: 0.8293 (t0) cc_final: 0.7802 (t0) REVERT: A 207 LEU cc_start: 0.7906 (tp) cc_final: 0.7474 (mt) REVERT: A 218 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7469 (tmt170) REVERT: B 27 MET cc_start: 0.5936 (OUTLIER) cc_final: 0.5662 (ppp) REVERT: B 37 ARG cc_start: 0.7389 (pmt170) cc_final: 0.6799 (ptt180) REVERT: B 193 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7714 (pp) REVERT: B 224 VAL cc_start: 0.6822 (OUTLIER) cc_final: 0.6440 (t) REVERT: B 299 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8285 (tttm) REVERT: B 300 PHE cc_start: 0.8351 (m-80) cc_final: 0.7516 (m-80) REVERT: B 343 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: B 405 ASN cc_start: 0.9120 (m110) cc_final: 0.8835 (m110) REVERT: B 418 LYS cc_start: 0.8813 (tptp) cc_final: 0.8455 (mttt) REVERT: C 73 ASN cc_start: 0.8881 (t0) cc_final: 0.8401 (t0) REVERT: C 104 TYR cc_start: 0.8273 (m-80) cc_final: 0.7992 (m-80) REVERT: C 107 ASN cc_start: 0.7513 (t0) cc_final: 0.7150 (t0) REVERT: C 140 TRP cc_start: 0.8614 (t60) cc_final: 0.8205 (t60) REVERT: C 160 ASP cc_start: 0.7496 (t0) cc_final: 0.7184 (t0) REVERT: C 189 PHE cc_start: 0.7978 (t80) cc_final: 0.7776 (t80) REVERT: C 204 ASP cc_start: 0.8202 (t0) cc_final: 0.7708 (t0) REVERT: C 207 LEU cc_start: 0.7908 (tp) cc_final: 0.7476 (mt) REVERT: C 218 ARG cc_start: 0.7978 (mtm110) cc_final: 0.7465 (tmt170) REVERT: D 27 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5706 (ppp) REVERT: D 37 ARG cc_start: 0.7389 (pmt170) cc_final: 0.6808 (ptt180) REVERT: D 193 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7704 (pp) REVERT: D 224 VAL cc_start: 0.6903 (OUTLIER) cc_final: 0.6526 (t) REVERT: D 299 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8283 (tttm) REVERT: D 300 PHE cc_start: 0.8345 (m-80) cc_final: 0.7510 (m-80) REVERT: D 343 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: D 405 ASN cc_start: 0.9129 (m110) cc_final: 0.8838 (m110) REVERT: D 418 LYS cc_start: 0.8809 (tptp) cc_final: 0.8451 (mttt) REVERT: E 73 ASN cc_start: 0.8877 (t0) cc_final: 0.8400 (t0) REVERT: E 104 TYR cc_start: 0.8245 (m-80) cc_final: 0.7849 (m-80) REVERT: E 107 ASN cc_start: 0.7519 (t0) cc_final: 0.7162 (t0) REVERT: E 126 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8238 (mt) REVERT: E 140 TRP cc_start: 0.8613 (t60) cc_final: 0.8199 (t60) REVERT: E 160 ASP cc_start: 0.7459 (t0) cc_final: 0.7254 (t0) REVERT: E 189 PHE cc_start: 0.7961 (t80) cc_final: 0.7750 (t80) REVERT: E 204 ASP cc_start: 0.8296 (t0) cc_final: 0.7804 (t0) REVERT: E 207 LEU cc_start: 0.7910 (tp) cc_final: 0.7478 (mt) REVERT: E 218 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7463 (tmt170) REVERT: F 27 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.5704 (ppp) REVERT: F 37 ARG cc_start: 0.7320 (pmt170) cc_final: 0.6838 (ptt180) REVERT: F 193 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7713 (pp) REVERT: F 224 VAL cc_start: 0.6903 (OUTLIER) cc_final: 0.6528 (t) REVERT: F 299 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8281 (tttm) REVERT: F 300 PHE cc_start: 0.8350 (m-80) cc_final: 0.7511 (m-80) REVERT: F 343 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: F 405 ASN cc_start: 0.9130 (m110) cc_final: 0.8837 (m110) REVERT: F 418 LYS cc_start: 0.8768 (tptp) cc_final: 0.8428 (mttt) REVERT: G 73 ASN cc_start: 0.8895 (t0) cc_final: 0.8418 (t0) REVERT: G 104 TYR cc_start: 0.8249 (m-80) cc_final: 0.7854 (m-80) REVERT: G 107 ASN cc_start: 0.7504 (t0) cc_final: 0.7147 (t0) REVERT: G 126 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8227 (mt) REVERT: G 140 TRP cc_start: 0.8624 (t60) cc_final: 0.8204 (t60) REVERT: G 160 ASP cc_start: 0.7471 (t0) cc_final: 0.7263 (t0) REVERT: G 189 PHE cc_start: 0.7965 (t80) cc_final: 0.7757 (t80) REVERT: G 204 ASP cc_start: 0.8297 (t0) cc_final: 0.7803 (t0) REVERT: G 207 LEU cc_start: 0.7906 (tp) cc_final: 0.7472 (mt) REVERT: G 218 ARG cc_start: 0.7975 (mtm110) cc_final: 0.7466 (tmt170) REVERT: H 27 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5675 (ppp) REVERT: H 37 ARG cc_start: 0.7331 (pmt170) cc_final: 0.6838 (ptt180) REVERT: H 193 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7716 (pp) REVERT: H 224 VAL cc_start: 0.6828 (OUTLIER) cc_final: 0.6448 (t) REVERT: H 299 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8288 (tttm) REVERT: H 300 PHE cc_start: 0.8357 (m-80) cc_final: 0.7517 (m-80) REVERT: H 343 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: H 405 ASN cc_start: 0.9148 (m-40) cc_final: 0.8876 (m110) REVERT: H 418 LYS cc_start: 0.8764 (tptp) cc_final: 0.8433 (mttt) outliers start: 79 outliers final: 32 residues processed: 533 average time/residue: 0.1467 time to fit residues: 118.2851 Evaluate side-chains 450 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 400 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 211 GLN Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 230 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN E 191 GLN G 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122885 restraints weight = 32360.497| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.47 r_work: 0.3458 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20200 Z= 0.133 Angle : 0.632 8.843 27328 Z= 0.319 Chirality : 0.041 0.158 3012 Planarity : 0.005 0.054 3468 Dihedral : 4.675 35.499 2684 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.82 % Allowed : 19.68 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.30 (0.17), residues: 2404 helix: -0.18 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : -1.97 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 183 TYR 0.010 0.001 TYR F 186 PHE 0.024 0.002 PHE B 191 TRP 0.007 0.001 TRP B 359 HIS 0.002 0.000 HIS F 481 Details of bonding type rmsd covalent geometry : bond 0.00313 (20200) covalent geometry : angle 0.63156 (27328) hydrogen bonds : bond 0.03460 ( 965) hydrogen bonds : angle 4.53008 ( 2739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 473 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8919 (t0) cc_final: 0.8423 (t0) REVERT: A 104 TYR cc_start: 0.8273 (m-80) cc_final: 0.7891 (m-80) REVERT: A 107 ASN cc_start: 0.7392 (t0) cc_final: 0.7037 (t0) REVERT: A 140 TRP cc_start: 0.8600 (t60) cc_final: 0.8194 (t60) REVERT: A 145 TYR cc_start: 0.8454 (m-10) cc_final: 0.8198 (m-10) REVERT: A 183 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.8093 (mtm-85) REVERT: A 207 LEU cc_start: 0.7840 (tp) cc_final: 0.7341 (mt) REVERT: A 218 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7483 (tmt170) REVERT: B 37 ARG cc_start: 0.7333 (pmt170) cc_final: 0.6998 (ptt180) REVERT: B 193 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7609 (pp) REVERT: B 224 VAL cc_start: 0.6762 (OUTLIER) cc_final: 0.6415 (t) REVERT: B 299 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8239 (tttm) REVERT: B 300 PHE cc_start: 0.8378 (m-80) cc_final: 0.7772 (m-80) REVERT: B 343 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: B 405 ASN cc_start: 0.9081 (m110) cc_final: 0.8799 (m110) REVERT: C 73 ASN cc_start: 0.8924 (t0) cc_final: 0.8430 (t0) REVERT: C 104 TYR cc_start: 0.8272 (m-80) cc_final: 0.7886 (m-80) REVERT: C 107 ASN cc_start: 0.7427 (t0) cc_final: 0.7045 (t0) REVERT: C 140 TRP cc_start: 0.8600 (t60) cc_final: 0.8193 (t60) REVERT: C 207 LEU cc_start: 0.7840 (tp) cc_final: 0.7343 (mt) REVERT: C 218 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7480 (tmt170) REVERT: D 37 ARG cc_start: 0.7331 (pmt170) cc_final: 0.7000 (ptt180) REVERT: D 193 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7600 (pp) REVERT: D 224 VAL cc_start: 0.6791 (OUTLIER) cc_final: 0.6452 (t) REVERT: D 299 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8238 (tttm) REVERT: D 300 PHE cc_start: 0.8378 (m-80) cc_final: 0.7773 (m-80) REVERT: D 343 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: D 405 ASN cc_start: 0.9086 (m110) cc_final: 0.8801 (m110) REVERT: E 73 ASN cc_start: 0.8917 (t0) cc_final: 0.8429 (t0) REVERT: E 104 TYR cc_start: 0.8270 (m-80) cc_final: 0.7887 (m-80) REVERT: E 107 ASN cc_start: 0.7430 (t0) cc_final: 0.7050 (t0) REVERT: E 140 TRP cc_start: 0.8587 (t60) cc_final: 0.8187 (t60) REVERT: E 207 LEU cc_start: 0.7842 (tp) cc_final: 0.7342 (mt) REVERT: E 218 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7481 (tmt170) REVERT: F 37 ARG cc_start: 0.7296 (pmt170) cc_final: 0.7048 (ptt180) REVERT: F 193 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7605 (pp) REVERT: F 224 VAL cc_start: 0.6792 (OUTLIER) cc_final: 0.6452 (t) REVERT: F 299 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8239 (tttm) REVERT: F 300 PHE cc_start: 0.8377 (m-80) cc_final: 0.7766 (m-80) REVERT: F 343 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: F 405 ASN cc_start: 0.9092 (m110) cc_final: 0.8804 (m110) REVERT: G 73 ASN cc_start: 0.8926 (t0) cc_final: 0.8435 (t0) REVERT: G 104 TYR cc_start: 0.8275 (m-80) cc_final: 0.7898 (m-80) REVERT: G 107 ASN cc_start: 0.7419 (t0) cc_final: 0.7032 (t0) REVERT: G 140 TRP cc_start: 0.8598 (t60) cc_final: 0.8194 (t60) REVERT: G 207 LEU cc_start: 0.7840 (tp) cc_final: 0.7334 (mt) REVERT: G 218 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7480 (tmt170) REVERT: H 37 ARG cc_start: 0.7305 (pmt170) cc_final: 0.7053 (ptt180) REVERT: H 193 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7610 (pp) REVERT: H 224 VAL cc_start: 0.6767 (OUTLIER) cc_final: 0.6418 (t) REVERT: H 299 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8239 (tttm) REVERT: H 300 PHE cc_start: 0.8385 (m-80) cc_final: 0.7770 (m-80) REVERT: H 343 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: H 405 ASN cc_start: 0.9108 (m-40) cc_final: 0.8834 (m110) outliers start: 82 outliers final: 33 residues processed: 537 average time/residue: 0.1535 time to fit residues: 123.4757 Evaluate side-chains 470 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 425 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 211 GLN Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 135 HIS E 135 HIS G 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.171489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125113 restraints weight = 32025.144| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.38 r_work: 0.3463 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20200 Z= 0.133 Angle : 0.645 8.788 27328 Z= 0.324 Chirality : 0.042 0.217 3012 Planarity : 0.005 0.057 3468 Dihedral : 4.500 22.110 2684 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.01 % Allowed : 20.29 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2404 helix: -0.01 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -1.91 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 183 TYR 0.012 0.001 TYR C 104 PHE 0.033 0.002 PHE A 142 TRP 0.007 0.001 TRP F 359 HIS 0.002 0.000 HIS B 481 Details of bonding type rmsd covalent geometry : bond 0.00317 (20200) covalent geometry : angle 0.64456 (27328) hydrogen bonds : bond 0.03355 ( 965) hydrogen bonds : angle 4.48571 ( 2739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 465 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8896 (t0) cc_final: 0.8390 (t0) REVERT: A 140 TRP cc_start: 0.8591 (t60) cc_final: 0.8184 (t60) REVERT: A 207 LEU cc_start: 0.8090 (tp) cc_final: 0.7712 (mt) REVERT: B 37 ARG cc_start: 0.7245 (pmt170) cc_final: 0.7032 (ptt180) REVERT: B 128 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8508 (tt) REVERT: B 193 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7637 (pp) REVERT: B 224 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.6395 (t) REVERT: B 300 PHE cc_start: 0.8429 (m-80) cc_final: 0.7779 (m-80) REVERT: B 343 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: B 405 ASN cc_start: 0.9067 (m110) cc_final: 0.8781 (m110) REVERT: C 73 ASN cc_start: 0.8906 (t0) cc_final: 0.8399 (t0) REVERT: C 97 ASP cc_start: 0.7331 (t0) cc_final: 0.7103 (t0) REVERT: C 140 TRP cc_start: 0.8586 (t60) cc_final: 0.8263 (t60) REVERT: C 207 LEU cc_start: 0.8103 (tp) cc_final: 0.7742 (mt) REVERT: D 37 ARG cc_start: 0.7243 (pmt170) cc_final: 0.7040 (ptt180) REVERT: D 128 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8507 (tt) REVERT: D 193 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7633 (pp) REVERT: D 224 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6431 (t) REVERT: D 300 PHE cc_start: 0.8428 (m-80) cc_final: 0.7784 (m-80) REVERT: D 343 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: D 405 ASN cc_start: 0.9081 (m110) cc_final: 0.8787 (m110) REVERT: E 73 ASN cc_start: 0.8890 (t0) cc_final: 0.8383 (t0) REVERT: E 97 ASP cc_start: 0.7303 (t0) cc_final: 0.7081 (t0) REVERT: E 140 TRP cc_start: 0.8593 (t60) cc_final: 0.8180 (t60) REVERT: E 207 LEU cc_start: 0.8094 (tp) cc_final: 0.7731 (mt) REVERT: F 128 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8497 (tt) REVERT: F 193 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7636 (pp) REVERT: F 224 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6432 (t) REVERT: F 300 PHE cc_start: 0.8424 (m-80) cc_final: 0.7788 (m-80) REVERT: F 343 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: F 405 ASN cc_start: 0.9081 (m110) cc_final: 0.8784 (m110) REVERT: G 73 ASN cc_start: 0.8913 (t0) cc_final: 0.8415 (t0) REVERT: G 97 ASP cc_start: 0.7287 (t0) cc_final: 0.7077 (t0) REVERT: G 140 TRP cc_start: 0.8597 (t60) cc_final: 0.8181 (t60) REVERT: G 207 LEU cc_start: 0.8096 (tp) cc_final: 0.7729 (mt) REVERT: H 128 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8499 (tt) REVERT: H 193 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7646 (pp) REVERT: H 224 VAL cc_start: 0.6769 (OUTLIER) cc_final: 0.6425 (t) REVERT: H 300 PHE cc_start: 0.8428 (m-80) cc_final: 0.7780 (m-80) REVERT: H 343 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: H 405 ASN cc_start: 0.9113 (m-40) cc_final: 0.8836 (m110) outliers start: 86 outliers final: 36 residues processed: 534 average time/residue: 0.1490 time to fit residues: 120.4665 Evaluate side-chains 471 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 419 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ILE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 216 optimal weight: 0.5980 chunk 222 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 230 optimal weight: 7.9990 chunk 198 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.173010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128646 restraints weight = 32195.584| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.78 r_work: 0.3446 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20200 Z= 0.120 Angle : 0.646 9.530 27328 Z= 0.322 Chirality : 0.041 0.177 3012 Planarity : 0.005 0.066 3468 Dihedral : 4.372 27.346 2684 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.94 % Allowed : 22.62 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2404 helix: 0.19 (0.14), residues: 1504 sheet: None (None), residues: 0 loop : -1.87 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 60 TYR 0.016 0.001 TYR C 104 PHE 0.033 0.002 PHE G 142 TRP 0.007 0.001 TRP D 359 HIS 0.001 0.000 HIS H 481 Details of bonding type rmsd covalent geometry : bond 0.00276 (20200) covalent geometry : angle 0.64604 (27328) hydrogen bonds : bond 0.03128 ( 965) hydrogen bonds : angle 4.38489 ( 2739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 458 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8907 (t0) cc_final: 0.8387 (t0) REVERT: A 140 TRP cc_start: 0.8580 (t60) cc_final: 0.8123 (t60) REVERT: A 183 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.8046 (mtt90) REVERT: A 207 LEU cc_start: 0.7995 (tp) cc_final: 0.7687 (mt) REVERT: A 217 MET cc_start: 0.7526 (mmm) cc_final: 0.7187 (mmm) REVERT: A 218 ARG cc_start: 0.7932 (mtm110) cc_final: 0.7566 (tmt170) REVERT: B 37 ARG cc_start: 0.7385 (pmt170) cc_final: 0.7181 (ptt180) REVERT: B 224 VAL cc_start: 0.6601 (OUTLIER) cc_final: 0.6263 (t) REVERT: B 268 MET cc_start: 0.7470 (tpp) cc_final: 0.6604 (ppp) REVERT: B 270 TYR cc_start: 0.6861 (t80) cc_final: 0.6625 (t80) REVERT: B 299 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8036 (tttp) REVERT: B 343 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: B 405 ASN cc_start: 0.9110 (m110) cc_final: 0.8796 (m110) REVERT: C 73 ASN cc_start: 0.8920 (t0) cc_final: 0.8399 (t0) REVERT: C 140 TRP cc_start: 0.8586 (t60) cc_final: 0.8131 (t60) REVERT: C 159 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6842 (mtp) REVERT: C 207 LEU cc_start: 0.7998 (tp) cc_final: 0.7689 (mt) REVERT: C 217 MET cc_start: 0.7529 (mmm) cc_final: 0.7204 (mmm) REVERT: C 218 ARG cc_start: 0.7937 (mtm110) cc_final: 0.7565 (tmt170) REVERT: D 224 VAL cc_start: 0.6604 (OUTLIER) cc_final: 0.6267 (t) REVERT: D 268 MET cc_start: 0.7474 (tpp) cc_final: 0.6608 (ppp) REVERT: D 270 TYR cc_start: 0.6866 (t80) cc_final: 0.6628 (t80) REVERT: D 299 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8030 (tttp) REVERT: D 343 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: D 405 ASN cc_start: 0.9109 (m110) cc_final: 0.8793 (m110) REVERT: E 73 ASN cc_start: 0.8892 (t0) cc_final: 0.8374 (t0) REVERT: E 183 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8072 (mtm-85) REVERT: E 207 LEU cc_start: 0.7993 (tp) cc_final: 0.7686 (mt) REVERT: E 217 MET cc_start: 0.7528 (mmm) cc_final: 0.7202 (mmm) REVERT: E 218 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7573 (tmt170) REVERT: F 224 VAL cc_start: 0.6599 (OUTLIER) cc_final: 0.6263 (t) REVERT: F 268 MET cc_start: 0.7476 (tpp) cc_final: 0.6616 (ppp) REVERT: F 270 TYR cc_start: 0.6848 (t80) cc_final: 0.6613 (t80) REVERT: F 299 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8028 (tttp) REVERT: F 343 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: F 405 ASN cc_start: 0.9090 (m110) cc_final: 0.8794 (m110) REVERT: G 73 ASN cc_start: 0.8889 (t0) cc_final: 0.8368 (t0) REVERT: G 183 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.8069 (mtm-85) REVERT: G 207 LEU cc_start: 0.7997 (tp) cc_final: 0.7685 (mt) REVERT: G 217 MET cc_start: 0.7518 (mmm) cc_final: 0.7189 (mmm) REVERT: G 218 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7570 (tmt170) REVERT: H 224 VAL cc_start: 0.6598 (OUTLIER) cc_final: 0.6264 (t) REVERT: H 270 TYR cc_start: 0.6782 (t80) cc_final: 0.6554 (t80) REVERT: H 299 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8031 (tttp) REVERT: H 343 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: H 405 ASN cc_start: 0.9140 (m-40) cc_final: 0.8863 (m110) outliers start: 63 outliers final: 31 residues processed: 505 average time/residue: 0.1481 time to fit residues: 113.2507 Evaluate side-chains 468 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 125 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 235 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN E 58 ASN G 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118680 restraints weight = 32279.304| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.33 r_work: 0.3384 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 20200 Z= 0.264 Angle : 0.744 9.093 27328 Z= 0.378 Chirality : 0.046 0.159 3012 Planarity : 0.006 0.064 3468 Dihedral : 4.874 26.321 2684 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.96 % Allowed : 22.29 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.17), residues: 2404 helix: -0.01 (0.14), residues: 1524 sheet: None (None), residues: 0 loop : -1.95 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 60 TYR 0.017 0.002 TYR H 271 PHE 0.031 0.003 PHE G 142 TRP 0.011 0.002 TRP H 170 HIS 0.005 0.001 HIS H 481 Details of bonding type rmsd covalent geometry : bond 0.00648 (20200) covalent geometry : angle 0.74441 (27328) hydrogen bonds : bond 0.04483 ( 965) hydrogen bonds : angle 4.87096 ( 2739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 408 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8841 (t0) cc_final: 0.8379 (t0) REVERT: A 207 LEU cc_start: 0.8000 (tp) cc_final: 0.7674 (mt) REVERT: A 218 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7555 (tmt170) REVERT: B 37 ARG cc_start: 0.7350 (pmt170) cc_final: 0.7135 (ptt180) REVERT: B 224 VAL cc_start: 0.6917 (OUTLIER) cc_final: 0.6608 (t) REVERT: B 299 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8220 (tttp) REVERT: B 405 ASN cc_start: 0.9036 (m110) cc_final: 0.8680 (m110) REVERT: C 73 ASN cc_start: 0.8846 (t0) cc_final: 0.8380 (t0) REVERT: C 82 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8654 (mt-10) REVERT: C 159 MET cc_start: 0.7442 (ttm) cc_final: 0.6727 (mtp) REVERT: C 207 LEU cc_start: 0.8006 (tp) cc_final: 0.7673 (mt) REVERT: C 218 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7569 (tmt170) REVERT: D 224 VAL cc_start: 0.6995 (OUTLIER) cc_final: 0.6670 (t) REVERT: D 299 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8160 (tttp) REVERT: D 343 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: D 405 ASN cc_start: 0.9046 (m110) cc_final: 0.8688 (m110) REVERT: E 73 ASN cc_start: 0.8867 (t0) cc_final: 0.8399 (t0) REVERT: E 82 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8660 (mt-10) REVERT: E 218 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7573 (tmt170) REVERT: F 224 VAL cc_start: 0.6996 (OUTLIER) cc_final: 0.6673 (t) REVERT: F 299 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8215 (tttp) REVERT: F 343 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: F 405 ASN cc_start: 0.9054 (m110) cc_final: 0.8719 (m110) REVERT: G 73 ASN cc_start: 0.8856 (t0) cc_final: 0.8391 (t0) REVERT: G 82 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: G 183 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.8036 (mtt90) REVERT: G 218 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7572 (tmt170) REVERT: H 224 VAL cc_start: 0.6919 (OUTLIER) cc_final: 0.6608 (t) REVERT: H 299 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8219 (tttp) REVERT: H 405 ASN cc_start: 0.9116 (m-40) cc_final: 0.8774 (m110) outliers start: 85 outliers final: 53 residues processed: 471 average time/residue: 0.1487 time to fit residues: 106.7875 Evaluate side-chains 457 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 395 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 211 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 211 GLN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 211 GLN Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 128 ILE Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 472 ILE Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 46 optimal weight: 8.9990 chunk 213 optimal weight: 0.0770 chunk 13 optimal weight: 4.9990 chunk 233 optimal weight: 0.0670 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.170116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125710 restraints weight = 31827.548| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.32 r_work: 0.3468 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20200 Z= 0.128 Angle : 0.692 9.219 27328 Z= 0.344 Chirality : 0.042 0.223 3012 Planarity : 0.005 0.061 3468 Dihedral : 4.521 30.485 2684 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.57 % Allowed : 23.65 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.17), residues: 2404 helix: 0.14 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -1.82 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 183 TYR 0.016 0.001 TYR A 104 PHE 0.030 0.002 PHE G 142 TRP 0.008 0.001 TRP B 8 HIS 0.001 0.000 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00292 (20200) covalent geometry : angle 0.69221 (27328) hydrogen bonds : bond 0.03287 ( 965) hydrogen bonds : angle 4.59701 ( 2739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 436 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8836 (t0) cc_final: 0.8369 (t0) REVERT: A 207 LEU cc_start: 0.8032 (tp) cc_final: 0.7748 (mt) REVERT: A 218 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7507 (tmt170) REVERT: B 224 VAL cc_start: 0.6651 (OUTLIER) cc_final: 0.6343 (t) REVERT: B 299 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8120 (tttp) REVERT: B 343 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: B 405 ASN cc_start: 0.9047 (m110) cc_final: 0.8742 (m110) REVERT: C 73 ASN cc_start: 0.8858 (t0) cc_final: 0.8391 (t0) REVERT: C 82 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: C 159 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6895 (mtp) REVERT: C 183 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.7713 (mpt180) REVERT: C 207 LEU cc_start: 0.8036 (tp) cc_final: 0.7743 (mt) REVERT: C 218 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7506 (tmt170) REVERT: D 224 VAL cc_start: 0.6752 (OUTLIER) cc_final: 0.6426 (t) REVERT: D 299 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8101 (tttp) REVERT: D 343 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: D 405 ASN cc_start: 0.9065 (m110) cc_final: 0.8758 (m110) REVERT: E 73 ASN cc_start: 0.8857 (t0) cc_final: 0.8391 (t0) REVERT: E 82 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: E 183 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.8105 (mtm-85) REVERT: E 207 LEU cc_start: 0.7747 (tp) cc_final: 0.7383 (mt) REVERT: E 218 ARG cc_start: 0.7844 (mtm110) cc_final: 0.7530 (tmt170) REVERT: F 224 VAL cc_start: 0.6755 (OUTLIER) cc_final: 0.6428 (t) REVERT: F 299 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8116 (tttp) REVERT: F 343 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: F 405 ASN cc_start: 0.9060 (m110) cc_final: 0.8743 (m110) REVERT: G 73 ASN cc_start: 0.8853 (t0) cc_final: 0.8385 (t0) REVERT: G 183 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8138 (mtm-85) REVERT: G 207 LEU cc_start: 0.7744 (tp) cc_final: 0.7378 (mt) REVERT: G 218 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7526 (tmt170) REVERT: H 224 VAL cc_start: 0.6658 (OUTLIER) cc_final: 0.6347 (t) REVERT: H 299 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8127 (tttp) REVERT: H 343 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: H 405 ASN cc_start: 0.9112 (m-40) cc_final: 0.8807 (m110) outliers start: 55 outliers final: 27 residues processed: 482 average time/residue: 0.1469 time to fit residues: 108.4748 Evaluate side-chains 457 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 419 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 chunk 129 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 180 optimal weight: 0.2980 chunk 203 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 138 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS C 135 HIS E 135 HIS G 135 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.169390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125131 restraints weight = 31956.805| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.48 r_work: 0.3446 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20200 Z= 0.142 Angle : 0.699 9.348 27328 Z= 0.351 Chirality : 0.043 0.174 3012 Planarity : 0.005 0.061 3468 Dihedral : 4.483 30.525 2684 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.38 % Allowed : 23.65 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2404 helix: 0.15 (0.14), residues: 1516 sheet: None (None), residues: 0 loop : -1.78 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 171 TYR 0.053 0.002 TYR D 270 PHE 0.028 0.002 PHE E 142 TRP 0.011 0.001 TRP H 170 HIS 0.002 0.000 HIS H 481 Details of bonding type rmsd covalent geometry : bond 0.00339 (20200) covalent geometry : angle 0.69936 (27328) hydrogen bonds : bond 0.03481 ( 965) hydrogen bonds : angle 4.63775 ( 2739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4808 Ramachandran restraints generated. 2404 Oldfield, 0 Emsley, 2404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 429 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8870 (t0) cc_final: 0.8391 (t0) REVERT: A 207 LEU cc_start: 0.8229 (tp) cc_final: 0.7883 (mt) REVERT: A 218 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7563 (tmt170) REVERT: B 224 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6414 (t) REVERT: B 299 LYS cc_start: 0.8558 (mtpt) cc_final: 0.8159 (tttp) REVERT: B 343 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: B 405 ASN cc_start: 0.9043 (m110) cc_final: 0.8745 (m110) REVERT: C 73 ASN cc_start: 0.8882 (t0) cc_final: 0.8414 (t0) REVERT: C 82 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8451 (mp0) REVERT: C 159 MET cc_start: 0.7299 (ttm) cc_final: 0.6684 (mtp) REVERT: C 207 LEU cc_start: 0.8234 (tp) cc_final: 0.7878 (mt) REVERT: C 218 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7558 (tmt170) REVERT: D 224 VAL cc_start: 0.6805 (OUTLIER) cc_final: 0.6522 (t) REVERT: D 343 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: D 405 ASN cc_start: 0.9045 (m110) cc_final: 0.8741 (m110) REVERT: E 73 ASN cc_start: 0.8895 (t0) cc_final: 0.8422 (t0) REVERT: E 82 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: E 183 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7958 (mtt90) REVERT: E 207 LEU cc_start: 0.7837 (tp) cc_final: 0.7510 (mt) REVERT: E 218 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7564 (tmt170) REVERT: F 148 MET cc_start: 0.6953 (tpt) cc_final: 0.6491 (mtt) REVERT: F 224 VAL cc_start: 0.6805 (OUTLIER) cc_final: 0.6520 (t) REVERT: F 299 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8155 (tttp) REVERT: F 343 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: F 405 ASN cc_start: 0.9073 (m110) cc_final: 0.8748 (m110) REVERT: G 73 ASN cc_start: 0.8884 (t0) cc_final: 0.8413 (t0) REVERT: G 82 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: G 183 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8053 (mtt90) REVERT: G 207 LEU cc_start: 0.7834 (tp) cc_final: 0.7505 (mt) REVERT: G 218 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7561 (tmt170) REVERT: H 224 VAL cc_start: 0.6714 (OUTLIER) cc_final: 0.6418 (t) REVERT: H 299 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8156 (tttp) REVERT: H 343 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: H 405 ASN cc_start: 0.9126 (m-40) cc_final: 0.8812 (m110) outliers start: 51 outliers final: 35 residues processed: 467 average time/residue: 0.1398 time to fit residues: 100.1011 Evaluate side-chains 461 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 415 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 479 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 124 optimal weight: 0.0980 chunk 237 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 139 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 HIS D 478 HIS F 478 HIS H 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.174256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128264 restraints weight = 32214.022| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.38 r_work: 0.3523 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20200 Z= 0.130 Angle : 0.689 9.615 27328 Z= 0.345 Chirality : 0.042 0.150 3012 Planarity : 0.005 0.059 3468 Dihedral : 4.318 31.110 2684 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.77 % Allowed : 24.86 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2404 helix: 0.31 (0.14), residues: 1492 sheet: None (None), residues: 0 loop : -1.55 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 171 TYR 0.066 0.001 TYR H 270 PHE 0.027 0.002 PHE D 191 TRP 0.013 0.001 TRP F 170 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00301 (20200) covalent geometry : angle 0.68938 (27328) hydrogen bonds : bond 0.03229 ( 965) hydrogen bonds : angle 4.49633 ( 2739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5580.99 seconds wall clock time: 96 minutes 21.86 seconds (5781.86 seconds total)