Starting phenix.real_space_refine on Sat Aug 23 22:40:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9udg_64069/08_2025/9udg_64069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9udg_64069/08_2025/9udg_64069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9udg_64069/08_2025/9udg_64069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9udg_64069/08_2025/9udg_64069.map" model { file = "/net/cci-nas-00/data/ceres_data/9udg_64069/08_2025/9udg_64069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9udg_64069/08_2025/9udg_64069.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9775 2.51 5 N 2447 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15132 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Chain: "B" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3173 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 395} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1558 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1507 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 381} Chain: "B" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 222 Unusual residues: {'0NI': 1, 'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9293 SG CYS D 112 45.353 75.231 65.173 1.00114.30 S ATOM 10259 SG CYS E 26 46.939 72.466 66.665 1.00107.90 S ATOM 8658 SG CYS D 29 45.683 69.191 62.480 1.00107.91 S ATOM 10977 SG CYS E 120 44.069 72.141 60.768 1.00113.74 S ATOM 12056 SG CYS F 70 47.040 93.868 89.262 1.00334.60 S ATOM 12103 SG CYS F 79 40.919 92.634 92.522 1.00293.30 S Time building chain proxies: 3.62, per 1000 atoms: 0.24 Number of scatterers: 15132 At special positions: 0 Unit cell: (90.64, 129.36, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2807 8.00 N 2447 7.00 C 9775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 558.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 70 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " Number of angles added : 8 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 12 sheets defined 54.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.639A pdb=" N THR A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 131 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.725A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.737A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.876A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 11 through 14 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.589A pdb=" N PHE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.586A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 152 removed outlier: 3.621A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.527A pdb=" N LEU B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.856A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.760A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.711A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.822A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'C' and resid 7 through 32 Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.648A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 92 through 99 removed outlier: 3.623A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU C 99 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.688A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.912A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 254 removed outlier: 3.870A pdb=" N ASP C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.598A pdb=" N LEU D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.507A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 removed outlier: 3.647A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.633A pdb=" N LEU D 107 " --> pdb=" O PHE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.832A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.875A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.639A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.185A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 64 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 98 Processing helix chain 'E' and resid 105 through 117 removed outlier: 3.630A pdb=" N ALA E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY E 110 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 113 " --> pdb=" O GLY E 110 " (cutoff:3.500A) Proline residue: E 114 - end of helix removed outlier: 3.821A pdb=" N THR E 117 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.930A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 removed outlier: 3.576A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.593A pdb=" N LEU F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 removed outlier: 3.764A pdb=" N PHE F 128 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 188 through 196 removed outlier: 3.997A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 244 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 4.145A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 343 through 347 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 Processing helix chain 'F' and resid 380 through 394 removed outlier: 4.241A pdb=" N ALA F 386 " --> pdb=" O MET F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 399 No H-bonds generated for 'chain 'F' and resid 397 through 399' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.791A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.597A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY A 74 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.151A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.182A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.616A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.659A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 49 removed outlier: 4.194A pdb=" N ILE F 35 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.041A pdb=" N GLN F 169 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.395A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 747 hydrogen bonds defined for protein. 2097 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: 1.93 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 6177 1.40 - 1.60: 9069 1.60 - 1.80: 133 1.80 - 2.00: 32 2.00 - 2.20: 8 Bond restraints: 15419 Sorted by residual: bond pdb=" C4 FMN C 301 " pdb=" C4A FMN C 301 " ideal model delta sigma weight residual 1.485 1.404 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C4 FMN B 600 " pdb=" C4A FMN B 600 " ideal model delta sigma weight residual 1.485 1.405 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" O5' FMN C 301 " pdb=" P FMN C 301 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O5' FMN B 600 " pdb=" P FMN B 600 " ideal model delta sigma weight residual 1.676 1.611 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C2 FMN C 301 " pdb=" N3 FMN C 301 " ideal model delta sigma weight residual 1.404 1.354 0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 15414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 20022 1.36 - 2.72: 720 2.72 - 4.08: 137 4.08 - 5.44: 15 5.44 - 6.81: 4 Bond angle restraints: 20898 Sorted by residual: angle pdb=" C SER D 102 " pdb=" CA SER D 102 " pdb=" CB SER D 102 " ideal model delta sigma weight residual 116.54 109.96 6.58 1.15e+00 7.56e-01 3.28e+01 angle pdb=" C VAL D 34 " pdb=" CA VAL D 34 " pdb=" CB VAL D 34 " ideal model delta sigma weight residual 112.19 107.68 4.51 1.15e+00 7.56e-01 1.54e+01 angle pdb=" N GLN C 116 " pdb=" CA GLN C 116 " pdb=" CB GLN C 116 " ideal model delta sigma weight residual 114.17 110.08 4.09 1.14e+00 7.69e-01 1.29e+01 angle pdb=" C GLN D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta sigma weight residual 121.70 127.26 -5.56 1.80e+00 3.09e-01 9.55e+00 angle pdb=" CA SER D 102 " pdb=" C SER D 102 " pdb=" N VAL D 103 " ideal model delta sigma weight residual 119.52 117.08 2.44 7.90e-01 1.60e+00 9.55e+00 ... (remaining 20893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 8957 34.80 - 69.61: 213 69.61 - 104.41: 15 104.41 - 139.22: 0 139.22 - 174.02: 2 Dihedral angle restraints: 9187 sinusoidal: 3756 harmonic: 5431 Sorted by residual: dihedral pdb=" CA LEU D 23 " pdb=" C LEU D 23 " pdb=" N GLN D 24 " pdb=" CA GLN D 24 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C3 PEE B 603 " pdb=" C1 PEE B 603 " pdb=" C2 PEE B 603 " pdb=" O3P PEE B 603 " ideal model delta sinusoidal sigma weight residual 62.73 -123.25 -174.02 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE B 603 " pdb=" C1 PEE B 603 " pdb=" C2 PEE B 603 " pdb=" O3P PEE B 603 " ideal model delta sinusoidal sigma weight residual -59.96 111.77 -171.73 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1405 0.028 - 0.057: 501 0.057 - 0.085: 242 0.085 - 0.113: 154 0.113 - 0.142: 46 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA VAL D 25 " pdb=" N VAL D 25 " pdb=" C VAL D 25 " pdb=" CB VAL D 25 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA TRP B 103 " pdb=" N TRP B 103 " pdb=" C TRP B 103 " pdb=" CB TRP B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CB THR B 127 " pdb=" CA THR B 127 " pdb=" OG1 THR B 127 " pdb=" CG2 THR B 127 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 2345 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 102 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO E 103 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 126 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO D 127 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 127 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 127 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 325 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO B 326 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " -0.023 5.00e-02 4.00e+02 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 161 2.62 - 3.19: 13811 3.19 - 3.76: 22237 3.76 - 4.33: 33338 4.33 - 4.90: 55226 Nonbonded interactions: 124773 Sorted by model distance: nonbonded pdb=" O PRO C 139 " pdb=" O HOH C 401 " model vdw 2.053 3.040 nonbonded pdb=" O ASP F 273 " pdb=" OD1 ASP F 273 " model vdw 2.097 3.040 nonbonded pdb=" NZ LYS E 36 " pdb=" O HOH E 401 " model vdw 2.110 3.120 nonbonded pdb=" OG SER D 30 " pdb=" OH TYR D 141 " model vdw 2.195 3.040 nonbonded pdb=" O LEU E 98 " pdb=" O PHE E 102 " model vdw 2.201 3.040 ... (remaining 124768 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 15425 Z= 0.180 Angle : 0.610 7.618 20906 Z= 0.353 Chirality : 0.044 0.142 2348 Planarity : 0.004 0.057 2612 Dihedral : 14.570 174.024 5723 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.26 % Allowed : 11.52 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.19), residues: 1907 helix: 1.42 (0.18), residues: 845 sheet: 0.13 (0.35), residues: 197 loop : -0.24 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 118 TYR 0.014 0.001 TYR E 106 PHE 0.015 0.001 PHE B 213 TRP 0.018 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00371 (15419) covalent geometry : angle 0.60694 (20898) hydrogen bonds : bond 0.14112 ( 747) hydrogen bonds : angle 5.53661 ( 2097) metal coordination : bond 0.00632 ( 6) metal coordination : angle 3.37025 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7205 (tp30) cc_final: 0.6699 (mt-10) REVERT: A 62 LYS cc_start: 0.6805 (mmmm) cc_final: 0.6411 (mmtp) REVERT: A 67 LYS cc_start: 0.7632 (mttt) cc_final: 0.7425 (mttm) REVERT: A 75 LYS cc_start: 0.7129 (ptmm) cc_final: 0.6830 (pttp) REVERT: A 138 LYS cc_start: 0.6913 (mtpm) cc_final: 0.6497 (mttt) REVERT: A 200 ARG cc_start: 0.6936 (mtp-110) cc_final: 0.6614 (mtp85) REVERT: A 212 ASP cc_start: 0.6651 (m-30) cc_final: 0.6413 (m-30) REVERT: A 233 ASP cc_start: 0.6771 (m-30) cc_final: 0.6566 (m-30) REVERT: A 259 GLN cc_start: 0.6760 (mp10) cc_final: 0.6181 (mm110) REVERT: A 284 GLU cc_start: 0.6647 (tt0) cc_final: 0.6435 (tt0) REVERT: A 342 LYS cc_start: 0.7282 (tttp) cc_final: 0.6792 (tmtt) REVERT: A 349 ARG cc_start: 0.7414 (mtm180) cc_final: 0.7035 (mtm180) REVERT: A 396 ASP cc_start: 0.6025 (m-30) cc_final: 0.5759 (m-30) REVERT: A 433 GLN cc_start: 0.5625 (tt0) cc_final: 0.4815 (pt0) REVERT: B 193 VAL cc_start: 0.6864 (t) cc_final: 0.6640 (m) REVERT: C 61 LYS cc_start: 0.5938 (pmtt) cc_final: 0.5599 (tttm) REVERT: C 109 GLU cc_start: 0.6457 (pm20) cc_final: 0.6127 (mp0) REVERT: C 112 LYS cc_start: 0.6593 (mttp) cc_final: 0.6124 (mtmt) REVERT: C 136 VAL cc_start: 0.7088 (t) cc_final: 0.6705 (p) REVERT: C 193 LYS cc_start: 0.7359 (mttp) cc_final: 0.6814 (mmtm) REVERT: C 204 LYS cc_start: 0.5549 (mmtp) cc_final: 0.5148 (mptt) REVERT: D 194 MET cc_start: 0.7028 (ttm) cc_final: 0.6609 (ttt) REVERT: F 29 LEU cc_start: 0.5617 (mt) cc_final: 0.5179 (tt) REVERT: F 125 GLU cc_start: 0.3687 (tm-30) cc_final: 0.3482 (mm-30) REVERT: F 163 ARG cc_start: 0.3228 (mtp180) cc_final: 0.2486 (tpp-160) REVERT: F 189 ARG cc_start: 0.6108 (tpp80) cc_final: 0.5704 (mmt180) REVERT: F 239 ASN cc_start: 0.3757 (p0) cc_final: 0.3349 (t0) REVERT: F 276 MET cc_start: 0.6024 (mtp) cc_final: 0.5618 (mtp) REVERT: F 289 ARG cc_start: 0.4454 (ttt-90) cc_final: 0.4205 (ttp80) outliers start: 4 outliers final: 1 residues processed: 279 average time/residue: 0.1245 time to fit residues: 49.0417 Evaluate side-chains 207 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS C 188 GLN C 216 HIS E 57 ASN F 367 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.166812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.094276 restraints weight = 130732.647| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 7.66 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15425 Z= 0.268 Angle : 0.741 10.073 20906 Z= 0.387 Chirality : 0.052 0.202 2348 Planarity : 0.006 0.060 2612 Dihedral : 10.286 174.037 2362 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.01 % Allowed : 10.31 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.19), residues: 1907 helix: 0.85 (0.17), residues: 862 sheet: 0.16 (0.36), residues: 186 loop : -0.42 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 408 TYR 0.018 0.002 TYR F 217 PHE 0.025 0.003 PHE B 213 TRP 0.023 0.003 TRP B 103 HIS 0.007 0.002 HIS F 367 Details of bonding type rmsd covalent geometry : bond 0.00661 (15419) covalent geometry : angle 0.73498 (20898) hydrogen bonds : bond 0.07158 ( 747) hydrogen bonds : angle 5.03017 ( 2097) metal coordination : bond 0.01237 ( 6) metal coordination : angle 4.92149 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7073 (tp30) cc_final: 0.6661 (mt-10) REVERT: A 75 LYS cc_start: 0.8377 (ptmm) cc_final: 0.8108 (ptpt) REVERT: A 200 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.7108 (mtp85) REVERT: A 259 GLN cc_start: 0.8111 (mp10) cc_final: 0.7758 (mm110) REVERT: A 284 GLU cc_start: 0.8180 (tt0) cc_final: 0.7936 (tt0) REVERT: A 333 GLU cc_start: 0.8138 (pt0) cc_final: 0.7576 (tt0) REVERT: A 342 LYS cc_start: 0.8361 (tttp) cc_final: 0.8118 (tmtt) REVERT: A 347 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8510 (t) REVERT: A 433 GLN cc_start: 0.7660 (tt0) cc_final: 0.7208 (pt0) REVERT: C 58 LYS cc_start: 0.7523 (mtpt) cc_final: 0.6665 (mtmt) REVERT: C 61 LYS cc_start: 0.6543 (pmtt) cc_final: 0.6156 (tttm) REVERT: C 69 LYS cc_start: 0.7300 (ttmm) cc_final: 0.7060 (ttpt) REVERT: C 95 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7273 (mtpp) REVERT: C 109 GLU cc_start: 0.6972 (pm20) cc_final: 0.6500 (mp0) REVERT: C 112 LYS cc_start: 0.7824 (mttp) cc_final: 0.7369 (mtmt) REVERT: C 136 VAL cc_start: 0.8634 (t) cc_final: 0.8333 (p) REVERT: C 193 LYS cc_start: 0.8401 (mttp) cc_final: 0.7884 (mmtm) REVERT: D 126 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: D 164 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6324 (tt0) REVERT: D 194 MET cc_start: 0.8433 (ttm) cc_final: 0.8066 (ttt) REVERT: E 10 LYS cc_start: 0.7933 (ttmm) cc_final: 0.7645 (ttpt) REVERT: E 52 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8410 (m) REVERT: E 92 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: F 82 LYS cc_start: 0.5253 (mmmt) cc_final: 0.4790 (mtpp) REVERT: F 142 ASN cc_start: 0.3422 (OUTLIER) cc_final: 0.3180 (t0) REVERT: F 163 ARG cc_start: 0.3430 (mtp180) cc_final: 0.2985 (tpp-160) REVERT: F 225 MET cc_start: 0.4462 (mpt) cc_final: 0.4044 (mpp) REVERT: F 245 MET cc_start: 0.5028 (tpp) cc_final: 0.4780 (tpt) REVERT: F 377 MET cc_start: 0.6507 (tmm) cc_final: 0.6233 (tmm) outliers start: 47 outliers final: 32 residues processed: 241 average time/residue: 0.1120 time to fit residues: 39.6479 Evaluate side-chains 242 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS C 216 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.171205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.100251 restraints weight = 129510.762| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 7.25 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15425 Z= 0.119 Angle : 0.540 8.866 20906 Z= 0.287 Chirality : 0.043 0.157 2348 Planarity : 0.005 0.051 2612 Dihedral : 9.637 168.837 2362 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.11 % Allowed : 11.65 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.19), residues: 1907 helix: 1.33 (0.18), residues: 863 sheet: 0.36 (0.37), residues: 185 loop : -0.35 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.015 0.001 TYR F 217 PHE 0.017 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00259 (15419) covalent geometry : angle 0.53700 (20898) hydrogen bonds : bond 0.04840 ( 747) hydrogen bonds : angle 4.59970 ( 2097) metal coordination : bond 0.00562 ( 6) metal coordination : angle 2.81443 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6972 (tp30) cc_final: 0.6600 (mt-10) REVERT: A 67 LYS cc_start: 0.8761 (mttt) cc_final: 0.8518 (mttm) REVERT: A 75 LYS cc_start: 0.8277 (ptmm) cc_final: 0.8029 (ptpt) REVERT: A 197 SER cc_start: 0.8824 (p) cc_final: 0.8350 (t) REVERT: A 200 ARG cc_start: 0.7362 (mtp-110) cc_final: 0.7078 (mtp85) REVERT: A 259 GLN cc_start: 0.8094 (mp10) cc_final: 0.7771 (mm110) REVERT: A 284 GLU cc_start: 0.7981 (tt0) cc_final: 0.7750 (tt0) REVERT: A 333 GLU cc_start: 0.8021 (pt0) cc_final: 0.7499 (tt0) REVERT: A 342 LYS cc_start: 0.8254 (tttp) cc_final: 0.7997 (tmtt) REVERT: A 347 VAL cc_start: 0.8658 (p) cc_final: 0.8452 (m) REVERT: A 396 ASP cc_start: 0.7866 (m-30) cc_final: 0.7572 (m-30) REVERT: A 433 GLN cc_start: 0.7636 (tt0) cc_final: 0.7142 (pt0) REVERT: B 403 ARG cc_start: 0.8344 (mtp180) cc_final: 0.8069 (mtp-110) REVERT: C 61 LYS cc_start: 0.6557 (pmtt) cc_final: 0.6184 (tttm) REVERT: C 69 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7325 (ttpt) REVERT: C 95 LYS cc_start: 0.7685 (mtpt) cc_final: 0.7305 (mtpp) REVERT: C 109 GLU cc_start: 0.6929 (pm20) cc_final: 0.6559 (mp0) REVERT: C 112 LYS cc_start: 0.7791 (mttp) cc_final: 0.7392 (mtmt) REVERT: C 136 VAL cc_start: 0.8791 (t) cc_final: 0.8490 (p) REVERT: C 193 LYS cc_start: 0.8340 (mttp) cc_final: 0.7965 (mmtm) REVERT: D 49 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8809 (mtm) REVERT: D 126 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: D 164 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6354 (tt0) REVERT: D 194 MET cc_start: 0.8457 (ttm) cc_final: 0.8071 (ttt) REVERT: E 10 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7598 (ttpt) REVERT: F 80 ARG cc_start: 0.5257 (ttp-170) cc_final: 0.4973 (ttp-170) REVERT: F 82 LYS cc_start: 0.5167 (mmmt) cc_final: 0.4695 (mtpp) REVERT: F 98 ILE cc_start: 0.3025 (OUTLIER) cc_final: 0.2501 (mp) REVERT: F 116 LYS cc_start: 0.5560 (OUTLIER) cc_final: 0.4740 (pptt) REVERT: F 142 ASN cc_start: 0.3362 (OUTLIER) cc_final: 0.3157 (t0) REVERT: F 163 ARG cc_start: 0.3265 (mtp180) cc_final: 0.2926 (tpp-160) REVERT: F 225 MET cc_start: 0.5084 (mpt) cc_final: 0.4669 (mpp) REVERT: F 368 GLU cc_start: 0.7193 (tt0) cc_final: 0.6906 (tp30) REVERT: F 377 MET cc_start: 0.6791 (tmm) cc_final: 0.6242 (tmm) REVERT: F 382 MET cc_start: 0.3975 (pp-130) cc_final: 0.2388 (pmm) outliers start: 33 outliers final: 14 residues processed: 227 average time/residue: 0.1123 time to fit residues: 37.6736 Evaluate side-chains 224 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.167901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.096248 restraints weight = 131108.308| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 7.43 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15425 Z= 0.216 Angle : 0.654 10.025 20906 Z= 0.340 Chirality : 0.048 0.191 2348 Planarity : 0.005 0.053 2612 Dihedral : 10.140 172.034 2359 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.01 % Allowed : 11.20 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.19), residues: 1907 helix: 0.95 (0.18), residues: 869 sheet: 0.23 (0.37), residues: 187 loop : -0.49 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 408 TYR 0.015 0.002 TYR D 141 PHE 0.022 0.002 PHE B 213 TRP 0.022 0.002 TRP B 103 HIS 0.005 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00527 (15419) covalent geometry : angle 0.64707 (20898) hydrogen bonds : bond 0.06430 ( 747) hydrogen bonds : angle 4.76618 ( 2097) metal coordination : bond 0.00871 ( 6) metal coordination : angle 4.80503 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.387 Fit side-chains REVERT: A 50 GLU cc_start: 0.7157 (tp30) cc_final: 0.6830 (mt-10) REVERT: A 75 LYS cc_start: 0.8483 (ptmm) cc_final: 0.8216 (ptpt) REVERT: A 200 ARG cc_start: 0.7510 (mtp-110) cc_final: 0.7246 (mtp85) REVERT: A 284 GLU cc_start: 0.7982 (tt0) cc_final: 0.7743 (tt0) REVERT: A 333 GLU cc_start: 0.8153 (pt0) cc_final: 0.7594 (tt0) REVERT: A 347 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8521 (t) REVERT: A 433 GLN cc_start: 0.7584 (tt0) cc_final: 0.7108 (pt0) REVERT: B 5 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.5710 (ttmm) REVERT: B 325 MET cc_start: 0.9263 (ttm) cc_final: 0.9029 (ttp) REVERT: C 61 LYS cc_start: 0.6491 (pmtt) cc_final: 0.6050 (tttm) REVERT: C 69 LYS cc_start: 0.7561 (ttmm) cc_final: 0.7283 (ttpt) REVERT: C 95 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7414 (mtpp) REVERT: C 109 GLU cc_start: 0.7006 (pm20) cc_final: 0.6485 (mp0) REVERT: C 112 LYS cc_start: 0.7913 (mttp) cc_final: 0.7520 (mtmt) REVERT: C 136 VAL cc_start: 0.8818 (t) cc_final: 0.8461 (p) REVERT: C 193 LYS cc_start: 0.8512 (mttp) cc_final: 0.8029 (mmtm) REVERT: D 87 ASP cc_start: 0.8094 (t0) cc_final: 0.7839 (t0) REVERT: D 126 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6637 (mm-30) REVERT: D 164 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6436 (tt0) REVERT: D 194 MET cc_start: 0.8338 (ttm) cc_final: 0.7925 (ttt) REVERT: E 10 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7651 (ttpt) REVERT: E 33 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7503 (mtpt) REVERT: E 92 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6930 (mt0) REVERT: F 82 LYS cc_start: 0.5211 (mmmt) cc_final: 0.4697 (mtpp) REVERT: F 98 ILE cc_start: 0.3296 (OUTLIER) cc_final: 0.2663 (mp) REVERT: F 142 ASN cc_start: 0.3452 (OUTLIER) cc_final: 0.3211 (t0) REVERT: F 163 ARG cc_start: 0.3356 (mtp180) cc_final: 0.3032 (tpp-160) REVERT: F 225 MET cc_start: 0.4936 (mpt) cc_final: 0.4679 (mpp) REVERT: F 368 GLU cc_start: 0.7304 (tt0) cc_final: 0.6926 (tp30) REVERT: F 377 MET cc_start: 0.6744 (tmm) cc_final: 0.6072 (tmm) REVERT: F 382 MET cc_start: 0.3685 (pp-130) cc_final: 0.2317 (pmm) outliers start: 47 outliers final: 31 residues processed: 237 average time/residue: 0.1046 time to fit residues: 36.6771 Evaluate side-chains 244 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 156 optimal weight: 30.0000 chunk 163 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 122 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 140 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.171404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.100662 restraints weight = 129417.383| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 7.24 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15425 Z= 0.117 Angle : 0.525 8.911 20906 Z= 0.277 Chirality : 0.042 0.160 2348 Planarity : 0.005 0.052 2612 Dihedral : 9.605 168.130 2359 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.62 % Allowed : 12.10 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.19), residues: 1907 helix: 1.38 (0.18), residues: 863 sheet: 0.35 (0.38), residues: 185 loop : -0.41 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.014 0.001 TYR F 217 PHE 0.017 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00253 (15419) covalent geometry : angle 0.52225 (20898) hydrogen bonds : bond 0.04642 ( 747) hydrogen bonds : angle 4.46079 ( 2097) metal coordination : bond 0.00468 ( 6) metal coordination : angle 2.85094 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.380 Fit side-chains REVERT: A 1 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7477 (tpt) REVERT: A 50 GLU cc_start: 0.7256 (tp30) cc_final: 0.6908 (mt-10) REVERT: A 67 LYS cc_start: 0.8814 (mttt) cc_final: 0.8550 (mttm) REVERT: A 75 LYS cc_start: 0.8414 (ptmm) cc_final: 0.8143 (ptpt) REVERT: A 200 ARG cc_start: 0.7424 (mtp-110) cc_final: 0.7184 (mtp85) REVERT: A 284 GLU cc_start: 0.8013 (tt0) cc_final: 0.7797 (tt0) REVERT: A 333 GLU cc_start: 0.8089 (pt0) cc_final: 0.7584 (tt0) REVERT: A 347 VAL cc_start: 0.8781 (p) cc_final: 0.8557 (m) REVERT: A 396 ASP cc_start: 0.7902 (m-30) cc_final: 0.7660 (m-30) REVERT: A 433 GLN cc_start: 0.7660 (tt0) cc_final: 0.7125 (pt0) REVERT: B 5 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.5767 (ttmm) REVERT: B 403 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7900 (mtp-110) REVERT: C 56 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7311 (tp30) REVERT: C 58 LYS cc_start: 0.7472 (mtpt) cc_final: 0.6614 (mtmt) REVERT: C 61 LYS cc_start: 0.6334 (pmtt) cc_final: 0.5952 (tttm) REVERT: C 69 LYS cc_start: 0.7421 (ttmm) cc_final: 0.7154 (ttpt) REVERT: C 109 GLU cc_start: 0.7062 (pm20) cc_final: 0.6558 (mp0) REVERT: C 112 LYS cc_start: 0.8033 (mttp) cc_final: 0.7711 (mttp) REVERT: C 136 VAL cc_start: 0.8846 (t) cc_final: 0.8494 (p) REVERT: C 193 LYS cc_start: 0.8346 (mttp) cc_final: 0.8001 (mmtm) REVERT: E 10 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7639 (ttpt) REVERT: E 92 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6705 (mt0) REVERT: E 95 GLU cc_start: 0.5433 (mt-10) cc_final: 0.4572 (mt-10) REVERT: F 82 LYS cc_start: 0.5112 (mmmt) cc_final: 0.4678 (mtpp) REVERT: F 98 ILE cc_start: 0.3048 (OUTLIER) cc_final: 0.2438 (mp) REVERT: F 102 GLU cc_start: 0.4980 (mp0) cc_final: 0.3879 (mp0) REVERT: F 116 LYS cc_start: 0.5302 (OUTLIER) cc_final: 0.5063 (tptt) REVERT: F 142 ASN cc_start: 0.3443 (OUTLIER) cc_final: 0.3220 (t0) REVERT: F 163 ARG cc_start: 0.3265 (mtp180) cc_final: 0.2931 (tpp-160) REVERT: F 225 MET cc_start: 0.5000 (mpt) cc_final: 0.4641 (mpp) REVERT: F 315 ARG cc_start: 0.3567 (ttp-170) cc_final: 0.2765 (ttp-110) REVERT: F 368 GLU cc_start: 0.7062 (tt0) cc_final: 0.6764 (tp30) REVERT: F 377 MET cc_start: 0.6743 (tmm) cc_final: 0.6481 (tmm) REVERT: F 382 MET cc_start: 0.3491 (pp-130) cc_final: 0.2240 (pmm) outliers start: 41 outliers final: 22 residues processed: 236 average time/residue: 0.1134 time to fit residues: 39.2569 Evaluate side-chains 229 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 23 optimal weight: 6.9990 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 156 optimal weight: 40.0000 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.165532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.093388 restraints weight = 130766.386| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 7.55 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15425 Z= 0.276 Angle : 0.710 11.562 20906 Z= 0.367 Chirality : 0.051 0.216 2348 Planarity : 0.006 0.058 2612 Dihedral : 10.475 175.348 2359 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.46 % Allowed : 11.78 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.19), residues: 1907 helix: 0.75 (0.17), residues: 875 sheet: 0.31 (0.39), residues: 184 loop : -0.58 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 134 TYR 0.017 0.002 TYR D 141 PHE 0.043 0.003 PHE F 267 TRP 0.022 0.003 TRP B 103 HIS 0.006 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00682 (15419) covalent geometry : angle 0.70234 (20898) hydrogen bonds : bond 0.07081 ( 747) hydrogen bonds : angle 4.84780 ( 2097) metal coordination : bond 0.01147 ( 6) metal coordination : angle 5.35091 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 0.498 Fit side-chains REVERT: A 50 GLU cc_start: 0.7085 (tp30) cc_final: 0.6681 (mt-10) REVERT: A 75 LYS cc_start: 0.8422 (ptmm) cc_final: 0.8080 (ptpt) REVERT: A 200 ARG cc_start: 0.7384 (mtp-110) cc_final: 0.7130 (mtp85) REVERT: A 284 GLU cc_start: 0.8323 (tt0) cc_final: 0.8108 (tt0) REVERT: A 333 GLU cc_start: 0.7987 (pt0) cc_final: 0.7523 (tt0) REVERT: A 347 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8578 (m) REVERT: A 433 GLN cc_start: 0.7622 (tt0) cc_final: 0.7209 (pt0) REVERT: B 5 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.5576 (ttmm) REVERT: C 58 LYS cc_start: 0.7592 (mtpt) cc_final: 0.6724 (mtmt) REVERT: C 61 LYS cc_start: 0.6413 (pmtt) cc_final: 0.5951 (tttm) REVERT: C 69 LYS cc_start: 0.7515 (ttmm) cc_final: 0.7249 (ttpt) REVERT: C 79 ASN cc_start: 0.7594 (m110) cc_final: 0.7391 (m-40) REVERT: C 95 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7239 (mtpp) REVERT: C 109 GLU cc_start: 0.7076 (pm20) cc_final: 0.6655 (mp0) REVERT: C 112 LYS cc_start: 0.8131 (mttp) cc_final: 0.7825 (mttp) REVERT: C 136 VAL cc_start: 0.8822 (t) cc_final: 0.8446 (p) REVERT: C 193 LYS cc_start: 0.8525 (mttp) cc_final: 0.8165 (mmtm) REVERT: D 164 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6315 (tt0) REVERT: E 10 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7533 (ttpt) REVERT: E 33 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7572 (mttm) REVERT: E 52 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8355 (m) REVERT: E 92 GLN cc_start: 0.6925 (OUTLIER) cc_final: 0.6683 (mt0) REVERT: F 82 LYS cc_start: 0.5128 (mmmt) cc_final: 0.4701 (mtpp) REVERT: F 98 ILE cc_start: 0.3134 (OUTLIER) cc_final: 0.2526 (mp) REVERT: F 102 GLU cc_start: 0.4897 (mp0) cc_final: 0.4438 (mp0) REVERT: F 116 LYS cc_start: 0.5409 (OUTLIER) cc_final: 0.5119 (tptt) REVERT: F 142 ASN cc_start: 0.3371 (OUTLIER) cc_final: 0.3127 (t0) REVERT: F 163 ARG cc_start: 0.3474 (mtp180) cc_final: 0.3090 (tpp-160) REVERT: F 225 MET cc_start: 0.4856 (mpt) cc_final: 0.4617 (mpp) REVERT: F 315 ARG cc_start: 0.3376 (ttp-170) cc_final: 0.2679 (ttp-110) REVERT: F 368 GLU cc_start: 0.7104 (tt0) cc_final: 0.6752 (tp30) REVERT: F 377 MET cc_start: 0.6778 (tmm) cc_final: 0.6497 (tmm) REVERT: F 382 MET cc_start: 0.2956 (pp-130) cc_final: 0.1862 (pmm) outliers start: 54 outliers final: 37 residues processed: 239 average time/residue: 0.1119 time to fit residues: 39.3104 Evaluate side-chains 244 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 186 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.170910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.100182 restraints weight = 131424.624| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 7.46 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15425 Z= 0.119 Angle : 0.526 8.894 20906 Z= 0.278 Chirality : 0.042 0.157 2348 Planarity : 0.005 0.061 2612 Dihedral : 9.770 170.731 2359 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.82 % Allowed : 13.00 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.19), residues: 1907 helix: 1.31 (0.18), residues: 863 sheet: 0.38 (0.39), residues: 184 loop : -0.48 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.015 0.001 TYR D 141 PHE 0.033 0.001 PHE F 267 TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00261 (15419) covalent geometry : angle 0.52337 (20898) hydrogen bonds : bond 0.04682 ( 747) hydrogen bonds : angle 4.45929 ( 2097) metal coordination : bond 0.00495 ( 6) metal coordination : angle 2.86797 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.375 Fit side-chains REVERT: A 50 GLU cc_start: 0.7034 (tp30) cc_final: 0.6681 (mt-10) REVERT: A 67 LYS cc_start: 0.8815 (mttt) cc_final: 0.8564 (mttm) REVERT: A 75 LYS cc_start: 0.8312 (ptmm) cc_final: 0.8031 (ptpt) REVERT: A 142 ILE cc_start: 0.8786 (mm) cc_final: 0.8572 (mm) REVERT: A 200 ARG cc_start: 0.7454 (mtp-110) cc_final: 0.7231 (mtp85) REVERT: A 284 GLU cc_start: 0.7977 (tt0) cc_final: 0.7731 (tt0) REVERT: A 333 GLU cc_start: 0.7905 (pt0) cc_final: 0.7423 (tt0) REVERT: A 433 GLN cc_start: 0.7530 (tt0) cc_final: 0.7166 (pt0) REVERT: B 5 LYS cc_start: 0.6793 (OUTLIER) cc_final: 0.5801 (ttmm) REVERT: B 403 ARG cc_start: 0.8318 (mtp180) cc_final: 0.7945 (mtp-110) REVERT: C 56 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7317 (tp30) REVERT: C 58 LYS cc_start: 0.7588 (mtpt) cc_final: 0.6706 (mtmt) REVERT: C 61 LYS cc_start: 0.6339 (pmtt) cc_final: 0.5915 (ttpt) REVERT: C 69 LYS cc_start: 0.7302 (ttmm) cc_final: 0.7043 (ttpt) REVERT: C 109 GLU cc_start: 0.7003 (pm20) cc_final: 0.6462 (mp0) REVERT: C 112 LYS cc_start: 0.8004 (mttp) cc_final: 0.7602 (mtmt) REVERT: C 136 VAL cc_start: 0.8860 (t) cc_final: 0.8493 (p) REVERT: C 193 LYS cc_start: 0.8461 (mttp) cc_final: 0.8030 (mmtm) REVERT: D 164 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6489 (tt0) REVERT: E 10 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7571 (ttpt) REVERT: E 33 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7556 (mttm) REVERT: E 52 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8078 (m) REVERT: E 92 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6921 (mt0) REVERT: E 95 GLU cc_start: 0.5501 (mt-10) cc_final: 0.4471 (mt-10) REVERT: F 55 LEU cc_start: 0.4869 (tp) cc_final: 0.4538 (mp) REVERT: F 82 LYS cc_start: 0.5061 (mmmt) cc_final: 0.4626 (mtpp) REVERT: F 98 ILE cc_start: 0.3193 (OUTLIER) cc_final: 0.2610 (mp) REVERT: F 102 GLU cc_start: 0.4940 (mp0) cc_final: 0.4468 (mp0) REVERT: F 142 ASN cc_start: 0.3479 (OUTLIER) cc_final: 0.3244 (t0) REVERT: F 163 ARG cc_start: 0.3523 (mtp180) cc_final: 0.3287 (tpp-160) REVERT: F 225 MET cc_start: 0.4765 (mpt) cc_final: 0.4446 (mpp) REVERT: F 315 ARG cc_start: 0.3378 (ttp-170) cc_final: 0.2732 (ttp-110) REVERT: F 368 GLU cc_start: 0.6994 (tt0) cc_final: 0.6788 (tp30) REVERT: F 377 MET cc_start: 0.6810 (tmm) cc_final: 0.6547 (tmm) REVERT: F 382 MET cc_start: 0.3211 (pp-130) cc_final: 0.1982 (pmm) outliers start: 44 outliers final: 25 residues processed: 232 average time/residue: 0.1141 time to fit residues: 38.8470 Evaluate side-chains 229 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.166610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.094291 restraints weight = 129061.747| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 7.39 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15425 Z= 0.206 Angle : 0.632 9.976 20906 Z= 0.328 Chirality : 0.047 0.185 2348 Planarity : 0.005 0.053 2612 Dihedral : 10.196 174.877 2359 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.88 % Allowed : 13.00 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.19), residues: 1907 helix: 1.00 (0.18), residues: 869 sheet: 0.32 (0.39), residues: 184 loop : -0.56 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 408 TYR 0.017 0.002 TYR D 141 PHE 0.022 0.002 PHE B 213 TRP 0.022 0.002 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00503 (15419) covalent geometry : angle 0.62510 (20898) hydrogen bonds : bond 0.06191 ( 747) hydrogen bonds : angle 4.66796 ( 2097) metal coordination : bond 0.00862 ( 6) metal coordination : angle 4.77731 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.379 Fit side-chains REVERT: A 50 GLU cc_start: 0.7119 (tp30) cc_final: 0.6691 (mt-10) REVERT: A 75 LYS cc_start: 0.8300 (ptmm) cc_final: 0.7977 (ptpt) REVERT: A 142 ILE cc_start: 0.8852 (mm) cc_final: 0.8566 (mm) REVERT: A 200 ARG cc_start: 0.7254 (mtp-110) cc_final: 0.6999 (mtp85) REVERT: A 284 GLU cc_start: 0.8187 (tt0) cc_final: 0.7974 (tt0) REVERT: A 333 GLU cc_start: 0.8046 (pt0) cc_final: 0.7627 (tt0) REVERT: A 433 GLN cc_start: 0.7704 (tt0) cc_final: 0.7280 (pt0) REVERT: B 5 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.5533 (ttmm) REVERT: C 56 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7279 (tp30) REVERT: C 58 LYS cc_start: 0.7658 (mtpt) cc_final: 0.6780 (mtmt) REVERT: C 61 LYS cc_start: 0.6387 (pmtt) cc_final: 0.5874 (ttpt) REVERT: C 69 LYS cc_start: 0.7345 (ttmm) cc_final: 0.7082 (ttpt) REVERT: C 95 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7677 (mtmt) REVERT: C 109 GLU cc_start: 0.7088 (pm20) cc_final: 0.6673 (mp0) REVERT: C 112 LYS cc_start: 0.8087 (mttp) cc_final: 0.7647 (mtmt) REVERT: C 136 VAL cc_start: 0.8801 (t) cc_final: 0.8414 (p) REVERT: C 193 LYS cc_start: 0.8625 (mttp) cc_final: 0.8127 (mmtm) REVERT: D 164 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6543 (tt0) REVERT: E 10 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7576 (ttpt) REVERT: E 33 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7696 (mttm) REVERT: E 52 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8390 (m) REVERT: E 92 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6899 (mt0) REVERT: F 82 LYS cc_start: 0.4973 (mmmt) cc_final: 0.4614 (mtpp) REVERT: F 102 GLU cc_start: 0.4809 (mp0) cc_final: 0.4067 (mp0) REVERT: F 142 ASN cc_start: 0.3530 (OUTLIER) cc_final: 0.3282 (t0) REVERT: F 163 ARG cc_start: 0.3827 (mtp180) cc_final: 0.3458 (tpp-160) REVERT: F 225 MET cc_start: 0.4599 (mpt) cc_final: 0.4303 (mpp) REVERT: F 315 ARG cc_start: 0.3224 (ttp-170) cc_final: 0.2686 (ttp-110) REVERT: F 368 GLU cc_start: 0.7084 (tt0) cc_final: 0.6834 (tp30) REVERT: F 377 MET cc_start: 0.6924 (tmm) cc_final: 0.6660 (tmm) REVERT: F 382 MET cc_start: 0.3068 (pp-130) cc_final: 0.1919 (pmm) REVERT: F 398 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6153 (tt0) outliers start: 45 outliers final: 34 residues processed: 233 average time/residue: 0.1107 time to fit residues: 37.8716 Evaluate side-chains 237 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 398 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 140 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 138 optimal weight: 0.0970 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN C 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.167262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.095188 restraints weight = 130402.377| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 7.40 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15425 Z= 0.177 Angle : 0.595 8.962 20906 Z= 0.311 Chirality : 0.045 0.172 2348 Planarity : 0.005 0.053 2612 Dihedral : 10.099 175.499 2359 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.62 % Allowed : 13.19 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 1907 helix: 1.08 (0.18), residues: 867 sheet: 0.33 (0.39), residues: 184 loop : -0.53 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.017 0.002 TYR F 167 PHE 0.023 0.002 PHE F 267 TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00427 (15419) covalent geometry : angle 0.58921 (20898) hydrogen bonds : bond 0.05711 ( 747) hydrogen bonds : angle 4.60046 ( 2097) metal coordination : bond 0.00751 ( 6) metal coordination : angle 4.18508 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.410 Fit side-chains REVERT: A 50 GLU cc_start: 0.7147 (tp30) cc_final: 0.6780 (mt-10) REVERT: A 75 LYS cc_start: 0.8406 (ptmm) cc_final: 0.8095 (ptpt) REVERT: A 142 ILE cc_start: 0.8814 (mm) cc_final: 0.8550 (mm) REVERT: A 200 ARG cc_start: 0.7435 (mtp-110) cc_final: 0.7197 (mtp85) REVERT: A 284 GLU cc_start: 0.8255 (tt0) cc_final: 0.8031 (tt0) REVERT: A 333 GLU cc_start: 0.7973 (pt0) cc_final: 0.7580 (tt0) REVERT: A 433 GLN cc_start: 0.7666 (tt0) cc_final: 0.7252 (pt0) REVERT: B 5 LYS cc_start: 0.6740 (OUTLIER) cc_final: 0.5683 (ttmm) REVERT: C 56 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7303 (tp30) REVERT: C 58 LYS cc_start: 0.7606 (mtpt) cc_final: 0.6762 (mtmt) REVERT: C 61 LYS cc_start: 0.6331 (pmtt) cc_final: 0.5840 (ttpt) REVERT: C 69 LYS cc_start: 0.7385 (ttmm) cc_final: 0.7111 (ttpt) REVERT: C 95 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7318 (mtpp) REVERT: C 109 GLU cc_start: 0.7042 (pm20) cc_final: 0.6739 (mp0) REVERT: C 112 LYS cc_start: 0.8057 (mttp) cc_final: 0.7603 (mtmt) REVERT: C 136 VAL cc_start: 0.8845 (t) cc_final: 0.8495 (p) REVERT: C 193 LYS cc_start: 0.8529 (mttp) cc_final: 0.8055 (mmtm) REVERT: D 164 GLU cc_start: 0.7046 (tp30) cc_final: 0.6394 (tt0) REVERT: E 10 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7513 (ttpt) REVERT: E 33 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7594 (mttm) REVERT: E 52 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8274 (m) REVERT: E 92 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.7008 (mt0) REVERT: E 95 GLU cc_start: 0.5614 (mt-10) cc_final: 0.4669 (mt-10) REVERT: F 82 LYS cc_start: 0.4983 (mmmt) cc_final: 0.4616 (mtpp) REVERT: F 102 GLU cc_start: 0.4897 (mp0) cc_final: 0.4114 (mp0) REVERT: F 142 ASN cc_start: 0.3715 (OUTLIER) cc_final: 0.3458 (t0) REVERT: F 163 ARG cc_start: 0.3703 (mtp180) cc_final: 0.3392 (tpp-160) REVERT: F 368 GLU cc_start: 0.7157 (tt0) cc_final: 0.6863 (tp30) REVERT: F 377 MET cc_start: 0.6893 (tmm) cc_final: 0.6625 (tmm) REVERT: F 382 MET cc_start: 0.2901 (pp-130) cc_final: 0.2095 (pmm) REVERT: F 398 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6239 (tt0) outliers start: 41 outliers final: 32 residues processed: 226 average time/residue: 0.1070 time to fit residues: 35.5162 Evaluate side-chains 235 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Chi-restraints excluded: chain F residue 398 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 156 optimal weight: 50.0000 chunk 168 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN C 79 ASN F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.167885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.095945 restraints weight = 129817.718| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 7.48 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15425 Z= 0.163 Angle : 0.582 8.930 20906 Z= 0.304 Chirality : 0.045 0.171 2348 Planarity : 0.005 0.054 2612 Dihedral : 10.006 175.190 2359 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.75 % Allowed : 13.25 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 1907 helix: 1.14 (0.18), residues: 868 sheet: 0.41 (0.38), residues: 195 loop : -0.52 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.019 0.002 TYR F 167 PHE 0.021 0.002 PHE F 267 TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00388 (15419) covalent geometry : angle 0.57698 (20898) hydrogen bonds : bond 0.05530 ( 747) hydrogen bonds : angle 4.56317 ( 2097) metal coordination : bond 0.00674 ( 6) metal coordination : angle 4.11964 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3814 Ramachandran restraints generated. 1907 Oldfield, 0 Emsley, 1907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.562 Fit side-chains REVERT: A 50 GLU cc_start: 0.7212 (tp30) cc_final: 0.6820 (mt-10) REVERT: A 75 LYS cc_start: 0.8292 (ptmm) cc_final: 0.7957 (ptpt) REVERT: A 142 ILE cc_start: 0.8854 (mm) cc_final: 0.8596 (mm) REVERT: A 200 ARG cc_start: 0.7383 (mtp-110) cc_final: 0.7166 (mtp85) REVERT: A 284 GLU cc_start: 0.7856 (tt0) cc_final: 0.7599 (tt0) REVERT: A 333 GLU cc_start: 0.8038 (pt0) cc_final: 0.7637 (tt0) REVERT: A 433 GLN cc_start: 0.7562 (tt0) cc_final: 0.7127 (pt0) REVERT: B 5 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.5644 (ttmm) REVERT: B 403 ARG cc_start: 0.8411 (mtp180) cc_final: 0.7997 (mtp-110) REVERT: C 56 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7282 (tp30) REVERT: C 58 LYS cc_start: 0.7581 (mtpt) cc_final: 0.6727 (mtmt) REVERT: C 61 LYS cc_start: 0.6276 (pmtt) cc_final: 0.5783 (ttpt) REVERT: C 69 LYS cc_start: 0.7313 (ttmm) cc_final: 0.7049 (ttpt) REVERT: C 95 LYS cc_start: 0.7835 (mtmt) cc_final: 0.7275 (mtpp) REVERT: C 109 GLU cc_start: 0.7018 (pm20) cc_final: 0.6708 (mp0) REVERT: C 112 LYS cc_start: 0.8132 (mttp) cc_final: 0.7674 (mtmt) REVERT: C 136 VAL cc_start: 0.8892 (t) cc_final: 0.8518 (p) REVERT: C 193 LYS cc_start: 0.8618 (mttp) cc_final: 0.8176 (mmtm) REVERT: D 164 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: E 10 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7554 (ttpt) REVERT: E 33 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7556 (mttm) REVERT: E 52 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8271 (m) REVERT: E 92 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6784 (mt0) REVERT: E 95 GLU cc_start: 0.5570 (mt-10) cc_final: 0.4601 (mt-10) REVERT: F 82 LYS cc_start: 0.5052 (mmmt) cc_final: 0.4627 (mtpp) REVERT: F 102 GLU cc_start: 0.4913 (mp0) cc_final: 0.4197 (mp0) REVERT: F 142 ASN cc_start: 0.3655 (OUTLIER) cc_final: 0.3387 (t0) REVERT: F 163 ARG cc_start: 0.3658 (mtp180) cc_final: 0.3345 (tpp-160) REVERT: F 317 MET cc_start: 0.5749 (mtm) cc_final: 0.5009 (mpp) REVERT: F 368 GLU cc_start: 0.7095 (tt0) cc_final: 0.6813 (tp30) REVERT: F 377 MET cc_start: 0.6825 (tmm) cc_final: 0.6556 (tmm) REVERT: F 382 MET cc_start: 0.2568 (pp-130) cc_final: 0.1922 (pmm) outliers start: 43 outliers final: 36 residues processed: 233 average time/residue: 0.1065 time to fit residues: 36.8349 Evaluate side-chains 240 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 109 GLN Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 335 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 173 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 179 optimal weight: 20.0000 chunk 138 optimal weight: 0.8980 chunk 174 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.168494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.097200 restraints weight = 128889.996| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 7.40 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15425 Z= 0.138 Angle : 0.561 8.908 20906 Z= 0.293 Chirality : 0.043 0.161 2348 Planarity : 0.005 0.055 2612 Dihedral : 9.865 174.354 2359 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.69 % Allowed : 13.44 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.53 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.19), residues: 1907 helix: 1.26 (0.18), residues: 868 sheet: 0.38 (0.38), residues: 195 loop : -0.51 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.019 0.001 TYR F 167 PHE 0.032 0.002 PHE F 267 TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00320 (15419) covalent geometry : angle 0.55620 (20898) hydrogen bonds : bond 0.05145 ( 747) hydrogen bonds : angle 4.49686 ( 2097) metal coordination : bond 0.00566 ( 6) metal coordination : angle 3.82915 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.17 seconds wall clock time: 37 minutes 54.63 seconds (2274.63 seconds total)