Starting phenix.real_space_refine on Tue Jun 17 06:58:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6n_32330/06_2025/7w6n_32330.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6n_32330/06_2025/7w6n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w6n_32330/06_2025/7w6n_32330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6n_32330/06_2025/7w6n_32330.map" model { file = "/net/cci-nas-00/data/ceres_data/7w6n_32330/06_2025/7w6n_32330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6n_32330/06_2025/7w6n_32330.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: D, F, H, C, E, G Time building chain proxies: 9.18, per 1000 atoms: 0.47 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: 4.99 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.85 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: 5.37 Time building geometry restraints manager: 5.86 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: 0.13 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.030 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- 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 : 18.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.003 TRP B 359 HIS 0.009 0.002 HIS B 481 PHE 0.024 0.003 PHE A 71 TYR 0.022 0.002 TYR H 270 ARG 0.006 0.001 ARG G 183 Details of bonding type rmsd hydrogen bonds : bond 0.17084 ( 965) hydrogen bonds : angle 7.07859 ( 2739) covalent geometry : bond 0.01097 (20200) covalent geometry : angle 0.89802 (27328) *********************** 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 : 2.310 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: 0.3615 time to fit residues: 244.0038 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 : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 58 ASN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.164673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116748 restraints weight = 32054.298| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.51 r_work: 0.3367 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20200 Z= 0.152 Angle : 0.665 9.161 27328 Z= 0.346 Chirality : 0.042 0.155 3012 Planarity : 0.005 0.058 3468 Dihedral : 5.335 35.903 2684 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.24 % Allowed : 16.14 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.16), residues: 2404 helix: -1.24 (0.12), residues: 1516 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 359 HIS 0.003 0.001 HIS B 481 PHE 0.014 0.002 PHE H 323 TYR 0.011 0.001 TYR H 270 ARG 0.003 0.000 ARG H 166 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 965) hydrogen bonds : angle 5.06241 ( 2739) covalent geometry : bond 0.00353 (20200) covalent geometry : angle 0.66521 (27328) *********************** 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 529 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 481 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8859 (t0) cc_final: 0.8365 (t0) REVERT: A 107 ASN cc_start: 0.7764 (t0) cc_final: 0.7448 (t0) REVERT: A 158 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7861 (ttt) REVERT: A 160 ASP cc_start: 0.7555 (t0) cc_final: 0.7218 (t0) REVERT: A 178 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7646 (mmmm) REVERT: A 183 ARG cc_start: 0.8866 (mmm-85) cc_final: 0.8177 (mtm180) REVERT: A 204 ASP cc_start: 0.8166 (t0) cc_final: 0.7746 (t0) REVERT: B 299 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8247 (tttp) REVERT: B 405 ASN cc_start: 0.9172 (m110) cc_final: 0.8902 (m110) REVERT: C 73 ASN cc_start: 0.8857 (t0) cc_final: 0.8363 (t0) REVERT: C 107 ASN cc_start: 0.7758 (t0) cc_final: 0.7443 (t0) REVERT: C 158 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7867 (ttt) REVERT: C 160 ASP cc_start: 0.7556 (t0) cc_final: 0.7220 (t0) REVERT: C 178 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7649 (mmmm) REVERT: C 183 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.8178 (mtm180) REVERT: C 204 ASP cc_start: 0.8184 (t0) cc_final: 0.7751 (t0) REVERT: D 299 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8243 (tttp) REVERT: D 405 ASN cc_start: 0.9169 (m110) cc_final: 0.8896 (m110) REVERT: E 73 ASN cc_start: 0.8856 (t0) cc_final: 0.8364 (t0) REVERT: E 107 ASN cc_start: 0.7768 (t0) cc_final: 0.7452 (t0) REVERT: E 158 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7861 (ttt) REVERT: E 160 ASP cc_start: 0.7580 (t0) cc_final: 0.7241 (t0) REVERT: E 178 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7648 (mmmm) REVERT: E 183 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8179 (mtm180) REVERT: E 204 ASP cc_start: 0.8186 (t0) cc_final: 0.7754 (t0) REVERT: F 299 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8243 (tttp) REVERT: F 405 ASN cc_start: 0.9167 (m110) cc_final: 0.8897 (m110) REVERT: G 73 ASN cc_start: 0.8851 (t0) cc_final: 0.8357 (t0) REVERT: G 107 ASN cc_start: 0.7762 (t0) cc_final: 0.7443 (t0) REVERT: G 158 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7854 (ttt) REVERT: G 160 ASP cc_start: 0.7572 (t0) cc_final: 0.7234 (t0) REVERT: G 178 LYS cc_start: 0.7870 (mmmm) cc_final: 0.7650 (mmmm) REVERT: G 183 ARG cc_start: 0.8874 (mmm-85) cc_final: 0.8179 (mtm180) REVERT: G 204 ASP cc_start: 0.8193 (t0) cc_final: 0.7761 (t0) REVERT: H 299 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8241 (tttp) REVERT: H 405 ASN cc_start: 0.9165 (m110) cc_final: 0.8900 (m110) outliers start: 48 outliers final: 16 residues processed: 513 average time/residue: 0.3540 time to fit residues: 269.4452 Evaluate side-chains 434 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 414 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 MET 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 126 LEU Chi-restraints excluded: chain C residue 158 MET 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 126 LEU Chi-restraints excluded: chain E residue 158 MET 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 126 LEU Chi-restraints excluded: chain G residue 158 MET 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 220 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.0770 chunk 106 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.170087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124012 restraints weight = 32127.958| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.39 r_work: 0.3440 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20200 Z= 0.146 Angle : 0.632 9.161 27328 Z= 0.325 Chirality : 0.042 0.149 3012 Planarity : 0.005 0.053 3468 Dihedral : 4.978 36.535 2684 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.47 % Allowed : 17.49 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2404 helix: -0.65 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -2.20 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 359 HIS 0.002 0.001 HIS D 481 PHE 0.028 0.002 PHE A 189 TYR 0.010 0.001 TYR D 186 ARG 0.003 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 965) hydrogen bonds : angle 4.75892 ( 2739) covalent geometry : bond 0.00339 (20200) covalent geometry : angle 0.63212 (27328) *********************** 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 529 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 476 time to evaluate : 2.236 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: 0.8866 (t0) cc_final: 0.8377 (t0) REVERT: A 107 ASN cc_start: 0.7626 (t0) cc_final: 0.7260 (t0) REVERT: A 139 ARG cc_start: 0.8366 (mtp180) cc_final: 0.8104 (ttp80) REVERT: A 140 TRP cc_start: 0.8621 (t60) cc_final: 0.8294 (t60) REVERT: A 159 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6988 (ttp) REVERT: A 160 ASP cc_start: 0.7470 (t0) cc_final: 0.7243 (t0) REVERT: A 193 MET cc_start: 0.5922 (mmt) cc_final: 0.5630 (mmt) REVERT: A 204 ASP cc_start: 0.8157 (t0) cc_final: 0.7659 (t0) REVERT: B 299 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8224 (tttp) REVERT: B 300 PHE cc_start: 0.8282 (m-80) cc_final: 0.7416 (m-80) REVERT: B 401 VAL cc_start: 0.9343 (m) cc_final: 0.9064 (m) REVERT: B 405 ASN cc_start: 0.9112 (m110) cc_final: 0.8794 (m110) REVERT: C 73 ASN cc_start: 0.8855 (t0) cc_final: 0.8362 (t0) REVERT: C 107 ASN cc_start: 0.7629 (t0) cc_final: 0.7267 (t0) REVERT: C 139 ARG cc_start: 0.8354 (mtp180) cc_final: 0.8091 (ttp80) REVERT: C 140 TRP cc_start: 0.8619 (t60) cc_final: 0.8295 (t60) REVERT: C 160 ASP cc_start: 0.7466 (t0) cc_final: 0.7230 (t0) REVERT: C 183 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8232 (mtt-85) REVERT: C 193 MET cc_start: 0.5928 (mmt) cc_final: 0.5634 (mmt) REVERT: C 204 ASP cc_start: 0.8156 (t0) cc_final: 0.7661 (t0) REVERT: D 299 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8222 (tttp) REVERT: D 300 PHE cc_start: 0.8281 (m-80) cc_final: 0.7416 (m-80) REVERT: D 401 VAL cc_start: 0.9341 (m) cc_final: 0.9058 (m) REVERT: D 405 ASN cc_start: 0.9108 (m110) cc_final: 0.8789 (m110) REVERT: E 73 ASN cc_start: 0.8843 (t0) cc_final: 0.8347 (t0) REVERT: E 107 ASN cc_start: 0.7641 (t0) cc_final: 0.7280 (t0) REVERT: E 139 ARG cc_start: 0.8375 (mtp180) cc_final: 0.8111 (ttp80) REVERT: E 140 TRP cc_start: 0.8614 (t60) cc_final: 0.8295 (t60) REVERT: E 159 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6994 (ttp) REVERT: E 160 ASP cc_start: 0.7478 (t0) cc_final: 0.7247 (t0) REVERT: E 193 MET cc_start: 0.5933 (mmt) cc_final: 0.5639 (mmt) REVERT: E 204 ASP cc_start: 0.8152 (t0) cc_final: 0.7658 (t0) REVERT: F 37 ARG cc_start: 0.7190 (pmt170) cc_final: 0.6571 (ptt90) REVERT: F 299 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8224 (tttp) REVERT: F 300 PHE cc_start: 0.8283 (m-80) cc_final: 0.7416 (m-80) REVERT: F 401 VAL cc_start: 0.9341 (m) cc_final: 0.9063 (m) REVERT: F 405 ASN cc_start: 0.9115 (m110) cc_final: 0.8792 (m110) REVERT: G 73 ASN cc_start: 0.8866 (t0) cc_final: 0.8374 (t0) REVERT: G 107 ASN cc_start: 0.7630 (t0) cc_final: 0.7267 (t0) REVERT: G 140 TRP cc_start: 0.8617 (t60) cc_final: 0.8300 (t60) REVERT: G 159 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6971 (ttp) REVERT: G 160 ASP cc_start: 0.7472 (t0) cc_final: 0.7243 (t0) REVERT: G 193 MET cc_start: 0.5927 (mmt) cc_final: 0.5636 (mmt) REVERT: G 204 ASP cc_start: 0.8159 (t0) cc_final: 0.7662 (t0) REVERT: H 37 ARG cc_start: 0.7198 (pmt170) cc_final: 0.6569 (ptt90) REVERT: H 299 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8229 (tttp) REVERT: H 300 PHE cc_start: 0.8281 (m-80) cc_final: 0.7415 (m-80) REVERT: H 401 VAL cc_start: 0.9349 (m) cc_final: 0.9070 (m) REVERT: H 405 ASN cc_start: 0.9112 (m110) cc_final: 0.8794 (m110) outliers start: 53 outliers final: 21 residues processed: 512 average time/residue: 0.3133 time to fit residues: 241.6892 Evaluate side-chains 449 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 425 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 159 MET 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 B residue 472 ILE 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 D residue 472 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 159 MET 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 F residue 472 ILE Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 159 MET Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 280 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 472 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 143 ASN A 196 ASN C 135 HIS C 143 ASN C 196 ASN E 135 HIS E 143 ASN E 196 ASN G 135 HIS G 196 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.168156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121252 restraints weight = 32730.985| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.73 r_work: 0.3432 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20200 Z= 0.161 Angle : 0.660 9.381 27328 Z= 0.330 Chirality : 0.042 0.148 3012 Planarity : 0.005 0.055 3468 Dihedral : 4.885 35.440 2684 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.59 % Allowed : 19.08 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2404 helix: -0.37 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -2.07 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 359 HIS 0.003 0.001 HIS B 481 PHE 0.030 0.002 PHE A 142 TYR 0.010 0.001 TYR D 186 ARG 0.006 0.000 ARG H 419 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 965) hydrogen bonds : angle 4.69307 ( 2739) covalent geometry : bond 0.00384 (20200) covalent geometry : angle 0.66008 (27328) *********************** 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 510 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 433 time to evaluate : 2.100 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: A 73 ASN cc_start: 0.8901 (t0) cc_final: 0.8413 (t0) REVERT: A 107 ASN cc_start: 0.7573 (t0) cc_final: 0.7372 (t0) REVERT: A 140 TRP cc_start: 0.8635 (t60) cc_final: 0.8222 (t60) REVERT: A 160 ASP cc_start: 0.7456 (t0) cc_final: 0.7244 (t0) REVERT: A 193 MET cc_start: 0.6732 (mmt) cc_final: 0.6343 (mmt) REVERT: A 204 ASP cc_start: 0.8147 (t0) cc_final: 0.7671 (t0) REVERT: A 207 LEU cc_start: 0.7405 (tt) cc_final: 0.6859 (mt) REVERT: A 218 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7469 (tmt170) REVERT: B 37 ARG cc_start: 0.7284 (pmt170) cc_final: 0.6740 (ptt180) REVERT: B 224 VAL cc_start: 0.7023 (OUTLIER) cc_final: 0.6723 (t) REVERT: B 343 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: B 401 VAL cc_start: 0.9357 (m) cc_final: 0.9068 (m) REVERT: B 405 ASN cc_start: 0.9116 (m110) cc_final: 0.8810 (m110) REVERT: C 73 ASN cc_start: 0.8891 (t0) cc_final: 0.8396 (t0) REVERT: C 107 ASN cc_start: 0.7575 (t0) cc_final: 0.7374 (t0) REVERT: C 140 TRP cc_start: 0.8633 (t60) cc_final: 0.8218 (t60) REVERT: C 159 MET cc_start: 0.7484 (ttm) cc_final: 0.6678 (ttp) REVERT: C 193 MET cc_start: 0.6733 (mmt) cc_final: 0.6340 (mmt) REVERT: C 204 ASP cc_start: 0.8153 (t0) cc_final: 0.7678 (t0) REVERT: C 207 LEU cc_start: 0.7401 (tt) cc_final: 0.6854 (mt) REVERT: C 218 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7467 (tmt170) REVERT: D 37 ARG cc_start: 0.7247 (pmt170) cc_final: 0.6725 (ptt180) REVERT: D 224 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6724 (t) REVERT: D 343 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: D 401 VAL cc_start: 0.9352 (m) cc_final: 0.9058 (m) REVERT: D 405 ASN cc_start: 0.9120 (m110) cc_final: 0.8812 (m110) REVERT: E 73 ASN cc_start: 0.8880 (t0) cc_final: 0.8387 (t0) REVERT: E 140 TRP cc_start: 0.8630 (t60) cc_final: 0.8220 (t60) REVERT: E 160 ASP cc_start: 0.7464 (t0) cc_final: 0.7249 (t0) REVERT: E 193 MET cc_start: 0.6739 (mmt) cc_final: 0.6348 (mmt) REVERT: E 204 ASP cc_start: 0.8152 (t0) cc_final: 0.7675 (t0) REVERT: E 207 LEU cc_start: 0.7404 (tt) cc_final: 0.6866 (mt) REVERT: E 218 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7461 (tmt170) REVERT: F 37 ARG cc_start: 0.7257 (pmt170) cc_final: 0.6866 (ptt180) REVERT: F 224 VAL cc_start: 0.7026 (OUTLIER) cc_final: 0.6728 (t) REVERT: F 343 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: F 401 VAL cc_start: 0.9351 (m) cc_final: 0.9057 (m) REVERT: F 405 ASN cc_start: 0.9113 (m110) cc_final: 0.8802 (m110) REVERT: G 73 ASN cc_start: 0.8899 (t0) cc_final: 0.8411 (t0) REVERT: G 107 ASN cc_start: 0.7576 (t0) cc_final: 0.7375 (t0) REVERT: G 140 TRP cc_start: 0.8627 (t60) cc_final: 0.8208 (t60) REVERT: G 160 ASP cc_start: 0.7466 (t0) cc_final: 0.7252 (t0) REVERT: G 193 MET cc_start: 0.6744 (mmt) cc_final: 0.6351 (mmt) REVERT: G 204 ASP cc_start: 0.8139 (t0) cc_final: 0.7662 (t0) REVERT: G 207 LEU cc_start: 0.7407 (tt) cc_final: 0.6860 (mt) REVERT: G 218 ARG cc_start: 0.7970 (mtm110) cc_final: 0.7466 (tmt170) REVERT: H 37 ARG cc_start: 0.7260 (pmt170) cc_final: 0.6868 (ptt180) REVERT: H 224 VAL cc_start: 0.7024 (OUTLIER) cc_final: 0.6723 (t) REVERT: H 343 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: H 401 VAL cc_start: 0.9363 (m) cc_final: 0.9073 (m) REVERT: H 405 ASN cc_start: 0.9114 (m110) cc_final: 0.8812 (m110) outliers start: 77 outliers final: 48 residues processed: 488 average time/residue: 0.3193 time to fit residues: 236.2196 Evaluate side-chains 462 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 406 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 234 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 373 MET 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 66 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 234 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 373 MET 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 66 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 234 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 373 MET 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 66 VAL Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 234 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 373 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 58 ASN G 135 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.164328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.116564 restraints weight = 32448.994| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.91 r_work: 0.3341 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20200 Z= 0.172 Angle : 0.657 8.863 27328 Z= 0.332 Chirality : 0.043 0.155 3012 Planarity : 0.005 0.057 3468 Dihedral : 4.827 34.733 2684 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.01 % Allowed : 20.15 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2404 helix: -0.17 (0.14), residues: 1500 sheet: None (None), residues: 0 loop : -1.95 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 359 HIS 0.003 0.001 HIS F 481 PHE 0.026 0.002 PHE H 191 TYR 0.011 0.001 TYR D 186 ARG 0.006 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 965) hydrogen bonds : angle 4.68656 ( 2739) covalent geometry : bond 0.00416 (20200) covalent geometry : angle 0.65734 (27328) *********************** 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 527 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 441 time to evaluate : 2.261 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: 0.8950 (t0) cc_final: 0.8473 (t0) REVERT: A 140 TRP cc_start: 0.8630 (t60) cc_final: 0.8209 (t60) REVERT: A 160 ASP cc_start: 0.7536 (t0) cc_final: 0.7261 (t0) REVERT: A 183 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8057 (mmt-90) REVERT: A 193 MET cc_start: 0.6836 (mmt) cc_final: 0.6409 (mmt) REVERT: A 207 LEU cc_start: 0.7510 (tt) cc_final: 0.6875 (mt) REVERT: A 218 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7497 (tmt170) REVERT: B 37 ARG cc_start: 0.7399 (pmt170) cc_final: 0.6918 (ptt180) REVERT: B 224 VAL cc_start: 0.7004 (OUTLIER) cc_final: 0.6704 (t) REVERT: B 299 LYS cc_start: 0.8894 (mtpt) cc_final: 0.8113 (tttp) REVERT: B 343 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: B 405 ASN cc_start: 0.9185 (m110) cc_final: 0.8968 (m-40) REVERT: C 73 ASN cc_start: 0.8946 (t0) cc_final: 0.8460 (t0) REVERT: C 107 ASN cc_start: 0.7551 (t0) cc_final: 0.7342 (t0) REVERT: C 183 ARG cc_start: 0.8815 (mmt-90) cc_final: 0.8176 (mtm-85) REVERT: C 193 MET cc_start: 0.6859 (mmt) cc_final: 0.6457 (mmt) REVERT: C 207 LEU cc_start: 0.7509 (tt) cc_final: 0.6881 (mt) REVERT: C 218 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7491 (tmt170) REVERT: D 37 ARG cc_start: 0.7411 (pmt170) cc_final: 0.6940 (ptt180) REVERT: D 224 VAL cc_start: 0.7004 (OUTLIER) cc_final: 0.6707 (t) REVERT: D 299 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8114 (tttp) REVERT: D 343 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: D 405 ASN cc_start: 0.9187 (m110) cc_final: 0.8856 (m110) REVERT: E 73 ASN cc_start: 0.8939 (t0) cc_final: 0.8458 (t0) REVERT: E 107 ASN cc_start: 0.7412 (t0) cc_final: 0.7162 (t0) REVERT: E 140 TRP cc_start: 0.8623 (t60) cc_final: 0.8203 (t60) REVERT: E 160 ASP cc_start: 0.7560 (t0) cc_final: 0.7283 (t0) REVERT: E 183 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8056 (mmt-90) REVERT: E 193 MET cc_start: 0.6839 (mmt) cc_final: 0.6413 (mmt) REVERT: E 207 LEU cc_start: 0.7516 (tt) cc_final: 0.6885 (mt) REVERT: E 218 ARG cc_start: 0.7997 (mtm110) cc_final: 0.7499 (tmt170) REVERT: F 37 ARG cc_start: 0.7380 (pmt170) cc_final: 0.7084 (ptt180) REVERT: F 224 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6712 (t) REVERT: F 299 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8110 (tttp) REVERT: F 343 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: F 405 ASN cc_start: 0.9178 (m110) cc_final: 0.8844 (m110) REVERT: G 73 ASN cc_start: 0.8939 (t0) cc_final: 0.8460 (t0) REVERT: G 140 TRP cc_start: 0.8638 (t60) cc_final: 0.8220 (t60) REVERT: G 160 ASP cc_start: 0.7549 (t0) cc_final: 0.7269 (t0) REVERT: G 183 ARG cc_start: 0.8355 (ttm-80) cc_final: 0.8078 (mmt-90) REVERT: G 193 MET cc_start: 0.6833 (mmt) cc_final: 0.6429 (mmt) REVERT: G 207 LEU cc_start: 0.7511 (tt) cc_final: 0.6874 (mt) REVERT: G 218 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7494 (tmt170) REVERT: H 37 ARG cc_start: 0.7385 (pmt170) cc_final: 0.7088 (ptt180) REVERT: H 224 VAL cc_start: 0.7007 (OUTLIER) cc_final: 0.6708 (t) REVERT: H 299 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8111 (tttp) REVERT: H 343 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7200 (tm-30) REVERT: H 405 ASN cc_start: 0.9182 (m110) cc_final: 0.8853 (m110) outliers start: 86 outliers final: 50 residues processed: 502 average time/residue: 0.3304 time to fit residues: 249.0106 Evaluate side-chains 468 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 410 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 234 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 373 MET 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 66 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 146 ARG Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 234 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 373 MET 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 66 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 234 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 373 MET 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 66 VAL Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 224 VAL Chi-restraints excluded: chain H residue 234 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 373 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.169915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123963 restraints weight = 32669.738| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.60 r_work: 0.3453 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20200 Z= 0.134 Angle : 0.648 8.851 27328 Z= 0.323 Chirality : 0.042 0.164 3012 Planarity : 0.005 0.057 3468 Dihedral : 4.597 29.573 2684 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.64 % Allowed : 19.50 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2404 helix: -0.02 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : -1.93 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 359 HIS 0.002 0.000 HIS H 481 PHE 0.023 0.002 PHE G 142 TYR 0.010 0.001 TYR C 104 ARG 0.004 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 965) hydrogen bonds : angle 4.55338 ( 2739) covalent geometry : bond 0.00315 (20200) covalent geometry : angle 0.64767 (27328) *********************** 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 527 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 449 time to evaluate : 2.328 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: 0.8911 (t0) cc_final: 0.8414 (t0) REVERT: A 107 ASN cc_start: 0.7313 (t0) cc_final: 0.7063 (t0) REVERT: A 140 TRP cc_start: 0.8592 (t60) cc_final: 0.8184 (t60) REVERT: A 183 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8088 (mmt-90) REVERT: A 207 LEU cc_start: 0.7497 (tt) cc_final: 0.6872 (mt) REVERT: B 37 ARG cc_start: 0.7235 (pmt170) cc_final: 0.7034 (ptt180) REVERT: B 299 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8092 (tttp) REVERT: B 343 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7266 (tm-30) REVERT: B 405 ASN cc_start: 0.9086 (m110) cc_final: 0.8785 (m110) REVERT: C 73 ASN cc_start: 0.8927 (t0) cc_final: 0.8426 (t0) REVERT: C 107 ASN cc_start: 0.7373 (t0) cc_final: 0.6958 (t0) REVERT: C 140 TRP cc_start: 0.8593 (t60) cc_final: 0.8189 (t60) REVERT: C 207 LEU cc_start: 0.7515 (tt) cc_final: 0.6960 (mt) REVERT: D 276 MET cc_start: 0.7355 (mmt) cc_final: 0.7052 (mmm) REVERT: D 299 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8101 (tttp) REVERT: D 343 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: D 405 ASN cc_start: 0.9099 (m110) cc_final: 0.8810 (m110) REVERT: E 73 ASN cc_start: 0.8915 (t0) cc_final: 0.8415 (t0) REVERT: E 107 ASN cc_start: 0.7303 (t0) cc_final: 0.7069 (t0) REVERT: E 140 TRP cc_start: 0.8582 (t60) cc_final: 0.8262 (t60) REVERT: E 183 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.8097 (mmt-90) REVERT: E 207 LEU cc_start: 0.7522 (tt) cc_final: 0.6968 (mt) REVERT: F 299 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8095 (tttp) REVERT: F 343 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: F 405 ASN cc_start: 0.9086 (m110) cc_final: 0.8779 (m110) REVERT: G 73 ASN cc_start: 0.8923 (t0) cc_final: 0.8428 (t0) REVERT: G 107 ASN cc_start: 0.7318 (t0) cc_final: 0.7072 (t0) REVERT: G 140 TRP cc_start: 0.8602 (t60) cc_final: 0.8191 (t60) REVERT: G 183 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.8103 (mmt-90) REVERT: G 207 LEU cc_start: 0.7505 (tt) cc_final: 0.6874 (mt) REVERT: H 128 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8520 (tt) REVERT: H 299 LYS cc_start: 0.8812 (mtpt) cc_final: 0.8098 (tttp) REVERT: H 343 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: H 405 ASN cc_start: 0.9089 (m110) cc_final: 0.8796 (m110) outliers start: 78 outliers final: 43 residues processed: 510 average time/residue: 0.3433 time to fit residues: 262.7791 Evaluate side-chains 453 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 405 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 126 GLU 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 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 C residue 126 LEU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 146 ARG 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 373 MET 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 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 126 GLU 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 472 ILE Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 128 ILE 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 343 GLU Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 373 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.172700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124815 restraints weight = 32690.878| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.51 r_work: 0.3474 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20200 Z= 0.124 Angle : 0.651 8.993 27328 Z= 0.326 Chirality : 0.041 0.173 3012 Planarity : 0.005 0.059 3468 Dihedral : 4.412 25.096 2684 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.17 % Allowed : 21.92 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2404 helix: 0.18 (0.14), residues: 1508 sheet: None (None), residues: 0 loop : -1.79 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 359 HIS 0.001 0.000 HIS F 481 PHE 0.034 0.002 PHE A 142 TYR 0.009 0.001 TYR H 186 ARG 0.003 0.000 ARG F 146 Details of bonding type rmsd hydrogen bonds : bond 0.03263 ( 965) hydrogen bonds : angle 4.45314 ( 2739) covalent geometry : bond 0.00287 (20200) covalent geometry : angle 0.65066 (27328) *********************** 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 498 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 430 time to evaluate : 2.119 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: A 73 ASN cc_start: 0.8903 (t0) cc_final: 0.8407 (t0) REVERT: A 82 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8407 (mp0) REVERT: A 107 ASN cc_start: 0.7216 (t0) cc_final: 0.6909 (t0) REVERT: A 140 TRP cc_start: 0.8589 (t60) cc_final: 0.8177 (t60) REVERT: A 159 MET cc_start: 0.7406 (ttm) cc_final: 0.6426 (ttp) REVERT: A 183 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8119 (mmt-90) REVERT: A 207 LEU cc_start: 0.7381 (tt) cc_final: 0.6902 (mt) REVERT: A 218 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7644 (tmt170) REVERT: B 128 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8521 (tt) REVERT: B 224 VAL cc_start: 0.6738 (OUTLIER) cc_final: 0.6399 (t) REVERT: B 299 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8055 (tttp) REVERT: B 343 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: B 405 ASN cc_start: 0.9045 (m110) cc_final: 0.8754 (m110) REVERT: B 418 LYS cc_start: 0.8765 (tptp) cc_final: 0.8402 (mttp) REVERT: C 73 ASN cc_start: 0.8912 (t0) cc_final: 0.8414 (t0) REVERT: C 82 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: C 140 TRP cc_start: 0.8583 (t60) cc_final: 0.8140 (t60) REVERT: C 183 ARG cc_start: 0.8605 (tpp-160) cc_final: 0.8091 (mtt180) REVERT: C 207 LEU cc_start: 0.7525 (tt) cc_final: 0.6913 (mt) REVERT: C 217 MET cc_start: 0.7393 (mmp) cc_final: 0.7071 (mmm) REVERT: C 218 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7636 (tmt170) REVERT: D 224 VAL cc_start: 0.6744 (OUTLIER) cc_final: 0.6408 (t) REVERT: D 299 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8062 (tttp) REVERT: D 343 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: D 405 ASN cc_start: 0.9064 (m110) cc_final: 0.8756 (m110) REVERT: E 73 ASN cc_start: 0.8891 (t0) cc_final: 0.8390 (t0) REVERT: E 82 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: E 107 ASN cc_start: 0.7204 (t0) cc_final: 0.6912 (t0) REVERT: E 126 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8129 (mt) REVERT: E 140 TRP cc_start: 0.8571 (t60) cc_final: 0.8158 (t60) REVERT: E 159 MET cc_start: 0.7458 (ttm) cc_final: 0.6503 (ttp) REVERT: E 183 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.8126 (mmt-90) REVERT: E 207 LEU cc_start: 0.7528 (tt) cc_final: 0.6963 (mt) REVERT: E 218 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7632 (tmt170) REVERT: F 224 VAL cc_start: 0.6741 (OUTLIER) cc_final: 0.6404 (t) REVERT: F 299 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8062 (tttp) REVERT: F 343 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: F 405 ASN cc_start: 0.9050 (m110) cc_final: 0.8749 (m110) REVERT: F 418 LYS cc_start: 0.8760 (tptp) cc_final: 0.8396 (mttp) REVERT: G 73 ASN cc_start: 0.8910 (t0) cc_final: 0.8417 (t0) REVERT: G 82 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: G 107 ASN cc_start: 0.7211 (t0) cc_final: 0.6916 (t0) REVERT: G 140 TRP cc_start: 0.8572 (t60) cc_final: 0.8158 (t60) REVERT: G 183 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.8118 (mmt-90) REVERT: G 207 LEU cc_start: 0.7384 (tt) cc_final: 0.6905 (mt) REVERT: G 217 MET cc_start: 0.7388 (mmp) cc_final: 0.7065 (mmm) REVERT: G 218 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7642 (tmt170) REVERT: H 224 VAL cc_start: 0.6743 (OUTLIER) cc_final: 0.6406 (t) REVERT: H 299 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8063 (tttp) REVERT: H 343 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: H 405 ASN cc_start: 0.9047 (m110) cc_final: 0.8749 (m110) REVERT: H 418 LYS cc_start: 0.8766 (tptp) cc_final: 0.8402 (mttp) outliers start: 68 outliers final: 41 residues processed: 483 average time/residue: 0.3238 time to fit residues: 235.5433 Evaluate side-chains 456 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 401 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 85 PHE 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 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 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 126 GLU 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 288 THR 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 472 ILE 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 E residue 126 LEU 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 288 THR Chi-restraints excluded: chain F residue 307 LEU 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 472 ILE 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 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 288 THR Chi-restraints excluded: chain H residue 307 LEU 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 472 ILE 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 80 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4200 r_free = 0.4200 target = 0.170844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124456 restraints weight = 32630.383| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.76 r_work: 0.3458 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 0.039 20200 Z= 0.127 Angle : 0.645 8.801 27328 Z= 0.324 Chirality : 0.041 0.181 3012 Planarity : 0.005 0.066 3468 Dihedral : 4.343 23.075 2684 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.06 % Allowed : 20.99 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.17), residues: 2404 helix: 0.22 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : -1.74 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 359 HIS 0.002 0.000 HIS D 481 PHE 0.033 0.002 PHE E 142 TYR 0.040 0.001 TYR H 270 ARG 0.003 0.000 ARG F 171 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 965) hydrogen bonds : angle 4.47425 ( 2739) covalent geometry : bond 0.00300 (20200) covalent geometry : angle 0.64453 (27328) *********************** 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 519 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 432 time to evaluate : 2.107 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: 0.8893 (t0) cc_final: 0.8407 (t0) REVERT: A 82 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: A 107 ASN cc_start: 0.7215 (t0) cc_final: 0.6893 (t0) REVERT: A 140 TRP cc_start: 0.8549 (t60) cc_final: 0.8086 (t60) REVERT: A 159 MET cc_start: 0.7419 (ttm) cc_final: 0.6485 (ttp) REVERT: A 183 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8101 (mmt-90) REVERT: A 207 LEU cc_start: 0.7345 (tt) cc_final: 0.6930 (mt) REVERT: A 218 ARG cc_start: 0.7906 (mtm110) cc_final: 0.7569 (tmt170) REVERT: B 128 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8532 (tt) REVERT: B 224 VAL cc_start: 0.6632 (OUTLIER) cc_final: 0.6346 (t) REVERT: B 276 MET cc_start: 0.6962 (mmm) cc_final: 0.6685 (mmm) REVERT: B 299 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8141 (tttp) REVERT: B 343 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: B 405 ASN cc_start: 0.8992 (m110) cc_final: 0.8721 (m110) REVERT: C 73 ASN cc_start: 0.8913 (t0) cc_final: 0.8426 (t0) REVERT: C 82 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: C 140 TRP cc_start: 0.8549 (t60) cc_final: 0.8095 (t60) REVERT: C 207 LEU cc_start: 0.7368 (tt) cc_final: 0.6906 (mt) REVERT: C 218 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7559 (tmt170) REVERT: D 224 VAL cc_start: 0.6636 (OUTLIER) cc_final: 0.6352 (t) REVERT: D 270 TYR cc_start: 0.6054 (t80) cc_final: 0.5779 (t80) REVERT: D 276 MET cc_start: 0.6976 (mmt) cc_final: 0.6632 (mmm) REVERT: D 299 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8145 (tttp) REVERT: D 343 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: D 405 ASN cc_start: 0.8997 (m110) cc_final: 0.8720 (m110) REVERT: E 73 ASN cc_start: 0.8882 (t0) cc_final: 0.8393 (t0) REVERT: E 82 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: E 107 ASN cc_start: 0.7216 (t0) cc_final: 0.6913 (t0) REVERT: E 126 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8180 (mt) REVERT: E 140 TRP cc_start: 0.8547 (t60) cc_final: 0.8085 (t60) REVERT: E 159 MET cc_start: 0.7417 (ttm) cc_final: 0.6478 (ttp) REVERT: E 183 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8098 (mmt-90) REVERT: E 207 LEU cc_start: 0.7329 (tt) cc_final: 0.6904 (mt) REVERT: E 218 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7574 (tmt170) REVERT: F 134 GLU cc_start: 0.7820 (pm20) cc_final: 0.7570 (pm20) REVERT: F 224 VAL cc_start: 0.6637 (OUTLIER) cc_final: 0.6352 (t) REVERT: F 270 TYR cc_start: 0.6025 (t80) cc_final: 0.5825 (t80) REVERT: F 276 MET cc_start: 0.6972 (mmm) cc_final: 0.6695 (mmm) REVERT: F 299 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8148 (tttp) REVERT: F 343 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: F 405 ASN cc_start: 0.8988 (m110) cc_final: 0.8713 (m110) REVERT: G 73 ASN cc_start: 0.8905 (t0) cc_final: 0.8417 (t0) REVERT: G 82 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: G 107 ASN cc_start: 0.7202 (t0) cc_final: 0.6897 (t0) REVERT: G 140 TRP cc_start: 0.8555 (t60) cc_final: 0.8097 (t60) REVERT: G 159 MET cc_start: 0.7383 (ttm) cc_final: 0.6476 (ttp) REVERT: G 183 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8112 (mmt-90) REVERT: G 207 LEU cc_start: 0.7348 (tt) cc_final: 0.6924 (mt) REVERT: G 218 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7562 (tmt170) REVERT: H 224 VAL cc_start: 0.6644 (OUTLIER) cc_final: 0.6360 (t) REVERT: H 270 TYR cc_start: 0.6048 (t80) cc_final: 0.5753 (t80) REVERT: H 276 MET cc_start: 0.6972 (mmm) cc_final: 0.6693 (mmm) REVERT: H 299 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8144 (tttp) REVERT: H 343 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: H 405 ASN cc_start: 0.8982 (m110) cc_final: 0.8713 (m110) outliers start: 87 outliers final: 47 residues processed: 499 average time/residue: 0.3256 time to fit residues: 244.7219 Evaluate side-chains 482 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 421 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 126 LEU 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 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 373 MET 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 66 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU 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 274 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 66 VAL Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 9 LEU 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 288 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 373 MET 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 66 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 9 LEU 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 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 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 230 optimal weight: 0.0670 chunk 17 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 149 optimal weight: 0.0370 chunk 184 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.174798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129360 restraints weight = 32159.320| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.37 r_work: 0.3528 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20200 Z= 0.118 Angle : 0.665 12.631 27328 Z= 0.330 Chirality : 0.040 0.181 3012 Planarity : 0.005 0.066 3468 Dihedral : 4.136 23.007 2684 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.31 % Allowed : 22.67 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2404 helix: 0.42 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -1.52 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 170 HIS 0.001 0.000 HIS G 135 PHE 0.030 0.002 PHE E 142 TYR 0.048 0.001 TYR B 270 ARG 0.003 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 965) hydrogen bonds : angle 4.35947 ( 2739) covalent geometry : bond 0.00268 (20200) covalent geometry : angle 0.66524 (27328) *********************** 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 544 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 473 time to evaluate : 2.101 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: 0.8832 (t0) cc_final: 0.8360 (t0) REVERT: A 82 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: A 91 GLN cc_start: 0.8742 (pt0) cc_final: 0.8360 (pm20) REVERT: A 183 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8068 (mpt-90) REVERT: A 207 LEU cc_start: 0.7284 (tt) cc_final: 0.6979 (mt) REVERT: A 218 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7592 (tmt170) REVERT: B 148 MET cc_start: 0.7132 (tpt) cc_final: 0.6818 (mtt) REVERT: B 224 VAL cc_start: 0.6825 (OUTLIER) cc_final: 0.6555 (t) REVERT: B 268 MET cc_start: 0.7161 (tpp) cc_final: 0.6386 (ppp) REVERT: B 343 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: B 401 VAL cc_start: 0.8986 (m) cc_final: 0.8626 (p) REVERT: B 405 ASN cc_start: 0.8926 (m110) cc_final: 0.8569 (m110) REVERT: C 73 ASN cc_start: 0.8836 (t0) cc_final: 0.8364 (t0) REVERT: C 82 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: C 91 GLN cc_start: 0.8742 (pt0) cc_final: 0.8354 (pm20) REVERT: C 126 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8063 (mt) REVERT: C 183 ARG cc_start: 0.8372 (tpp-160) cc_final: 0.8012 (mtt90) REVERT: C 207 LEU cc_start: 0.7276 (tt) cc_final: 0.6984 (mt) REVERT: C 218 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7514 (tmt170) REVERT: D 224 VAL cc_start: 0.6588 (OUTLIER) cc_final: 0.6256 (t) REVERT: D 268 MET cc_start: 0.7372 (tpp) cc_final: 0.6629 (ppp) REVERT: D 270 TYR cc_start: 0.6391 (t80) cc_final: 0.6057 (t80) REVERT: D 276 MET cc_start: 0.7070 (mmt) cc_final: 0.6844 (mmm) REVERT: D 343 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: D 401 VAL cc_start: 0.8977 (m) cc_final: 0.8617 (p) REVERT: D 405 ASN cc_start: 0.8933 (m110) cc_final: 0.8572 (m110) REVERT: E 73 ASN cc_start: 0.8802 (t0) cc_final: 0.8327 (t0) REVERT: E 91 GLN cc_start: 0.8728 (pt0) cc_final: 0.8346 (pm20) REVERT: E 207 LEU cc_start: 0.7276 (tt) cc_final: 0.6979 (mt) REVERT: E 218 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7568 (tmt170) REVERT: F 148 MET cc_start: 0.7145 (tpt) cc_final: 0.6858 (mtt) REVERT: F 224 VAL cc_start: 0.6587 (OUTLIER) cc_final: 0.6254 (t) REVERT: F 270 TYR cc_start: 0.5977 (t80) cc_final: 0.5748 (t80) REVERT: F 276 MET cc_start: 0.7026 (mmm) cc_final: 0.6776 (mmm) REVERT: F 343 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: F 401 VAL cc_start: 0.8978 (m) cc_final: 0.8625 (p) REVERT: F 405 ASN cc_start: 0.8923 (m110) cc_final: 0.8564 (m110) REVERT: G 73 ASN cc_start: 0.8797 (t0) cc_final: 0.8325 (t0) REVERT: G 82 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: G 91 GLN cc_start: 0.8742 (pt0) cc_final: 0.8359 (pm20) REVERT: G 183 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8065 (mpt-90) REVERT: G 207 LEU cc_start: 0.7296 (tt) cc_final: 0.6977 (mt) REVERT: G 218 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7507 (tmt170) REVERT: H 224 VAL cc_start: 0.6596 (OUTLIER) cc_final: 0.6264 (t) REVERT: H 270 TYR cc_start: 0.6616 (t80) cc_final: 0.6260 (t80) REVERT: H 276 MET cc_start: 0.7060 (mmm) cc_final: 0.6773 (mmm) REVERT: H 310 LEU cc_start: 0.8910 (tp) cc_final: 0.8701 (tt) REVERT: H 343 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: H 401 VAL cc_start: 0.8991 (m) cc_final: 0.8631 (p) REVERT: H 405 ASN cc_start: 0.8942 (m110) cc_final: 0.8584 (m110) outliers start: 71 outliers final: 31 residues processed: 529 average time/residue: 0.3290 time to fit residues: 261.5721 Evaluate side-chains 491 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 448 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 82 GLU 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 288 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 126 LEU 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 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 66 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 126 GLU 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 288 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 126 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 139 optimal weight: 0.0980 chunk 214 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 82 optimal weight: 0.3980 chunk 181 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.172479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125772 restraints weight = 32136.162| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.39 r_work: 0.3487 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20200 Z= 0.136 Angle : 0.680 9.169 27328 Z= 0.342 Chirality : 0.042 0.200 3012 Planarity : 0.005 0.072 3468 Dihedral : 4.176 20.034 2684 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.57 % Allowed : 23.83 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.17), residues: 2404 helix: 0.36 (0.14), residues: 1488 sheet: None (None), residues: 0 loop : -1.47 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 170 HIS 0.002 0.000 HIS F 481 PHE 0.026 0.002 PHE G 142 TYR 0.039 0.001 TYR B 270 ARG 0.006 0.000 ARG H 171 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 965) hydrogen bonds : angle 4.49369 ( 2739) covalent geometry : bond 0.00324 (20200) covalent geometry : angle 0.68001 (27328) ********************** 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 494 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 439 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASN cc_start: 0.8761 (t0) cc_final: 0.8279 (t0) REVERT: A 74 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7297 (tp30) REVERT: A 159 MET cc_start: 0.7377 (ptp) cc_final: 0.6730 (ptm) REVERT: A 207 LEU cc_start: 0.7288 (tt) cc_final: 0.7005 (mt) REVERT: A 218 ARG cc_start: 0.7876 (mtm110) cc_final: 0.7570 (tmt170) REVERT: B 128 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8520 (tt) REVERT: B 148 MET cc_start: 0.7217 (tpt) cc_final: 0.6894 (mtt) REVERT: B 224 VAL cc_start: 0.6888 (OUTLIER) cc_final: 0.6617 (t) REVERT: B 230 ASP cc_start: 0.6364 (t70) cc_final: 0.5800 (t70) REVERT: B 268 MET cc_start: 0.7037 (tpp) cc_final: 0.6291 (ppp) REVERT: B 299 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8018 (tttp) REVERT: B 343 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: B 401 VAL cc_start: 0.8991 (m) cc_final: 0.8628 (p) REVERT: B 405 ASN cc_start: 0.8921 (m110) cc_final: 0.8566 (m110) REVERT: C 73 ASN cc_start: 0.8792 (t0) cc_final: 0.8310 (t0) REVERT: C 74 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7266 (tp30) REVERT: C 183 ARG cc_start: 0.8351 (tpp-160) cc_final: 0.8037 (mtt90) REVERT: C 207 LEU cc_start: 0.7273 (tt) cc_final: 0.7009 (mt) REVERT: C 218 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7506 (tmt170) REVERT: D 148 MET cc_start: 0.7253 (tpt) cc_final: 0.6874 (mtt) REVERT: D 224 VAL cc_start: 0.6734 (OUTLIER) cc_final: 0.6433 (t) REVERT: D 270 TYR cc_start: 0.6609 (t80) cc_final: 0.6301 (t80) REVERT: D 299 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8037 (tttp) REVERT: D 343 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: D 401 VAL cc_start: 0.8985 (m) cc_final: 0.8617 (p) REVERT: D 405 ASN cc_start: 0.8924 (m110) cc_final: 0.8558 (m110) REVERT: E 73 ASN cc_start: 0.8764 (t0) cc_final: 0.8285 (t0) REVERT: E 74 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7302 (tp30) REVERT: E 159 MET cc_start: 0.7488 (ptm) cc_final: 0.7278 (ptp) REVERT: E 207 LEU cc_start: 0.7259 (tt) cc_final: 0.6997 (mt) REVERT: E 218 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7592 (tmt170) REVERT: F 148 MET cc_start: 0.7163 (tpt) cc_final: 0.6848 (mtt) REVERT: F 224 VAL cc_start: 0.6737 (OUTLIER) cc_final: 0.6436 (t) REVERT: F 270 TYR cc_start: 0.6169 (t80) cc_final: 0.5888 (t80) REVERT: F 299 LYS cc_start: 0.8343 (mtpt) cc_final: 0.8042 (tttp) REVERT: F 343 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: F 401 VAL cc_start: 0.8981 (m) cc_final: 0.8622 (p) REVERT: F 405 ASN cc_start: 0.8915 (m110) cc_final: 0.8552 (m110) REVERT: G 73 ASN cc_start: 0.8742 (t0) cc_final: 0.8265 (t0) REVERT: G 74 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7304 (tp30) REVERT: G 207 LEU cc_start: 0.7277 (tt) cc_final: 0.7002 (mt) REVERT: G 218 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7501 (tmt170) REVERT: H 224 VAL cc_start: 0.6786 (OUTLIER) cc_final: 0.6488 (t) REVERT: H 270 TYR cc_start: 0.6605 (t80) cc_final: 0.6237 (t80) REVERT: H 299 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8035 (tttp) REVERT: H 343 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: H 401 VAL cc_start: 0.9003 (m) cc_final: 0.8632 (p) REVERT: H 405 ASN cc_start: 0.8928 (m110) cc_final: 0.8568 (m110) outliers start: 55 outliers final: 40 residues processed: 479 average time/residue: 0.3506 time to fit residues: 254.1186 Evaluate side-chains 479 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 430 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 85 PHE 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 288 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 126 GLU 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 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 E residue 66 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 126 GLU 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 288 THR Chi-restraints excluded: chain F residue 343 GLU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 126 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.0770 chunk 153 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.130314 restraints weight = 32343.748| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.59 r_work: 0.3489 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20200 Z= 0.125 Angle : 0.683 9.623 27328 Z= 0.342 Chirality : 0.041 0.195 3012 Planarity : 0.005 0.065 3468 Dihedral : 4.087 20.496 2684 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.38 % Allowed : 24.16 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2404 helix: 0.37 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -1.32 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 170 HIS 0.002 0.000 HIS A 185 PHE 0.027 0.002 PHE G 142 TYR 0.032 0.001 TYR D 270 ARG 0.008 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 965) hydrogen bonds : angle 4.43292 ( 2739) covalent geometry : bond 0.00292 (20200) covalent geometry : angle 0.68272 (27328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11773.27 seconds wall clock time: 202 minutes 18.51 seconds (12138.51 seconds total)