Starting phenix.real_space_refine on Fri Jul 3 18:48:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk5_33244/07_2026/7xk5_33244.cif" } resolution = 3.1 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= 0.091 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 9608 2.51 5 N 2409 2.21 5 O 2714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14834 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} 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: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3153 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 194 Unusual residues: {'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9093 SG CYS D 112 42.766 75.174 64.039 1.00 43.00 S ATOM 10059 SG CYS E 26 44.768 71.143 65.164 1.00 32.42 S ATOM 8454 SG CYS D 29 43.082 68.001 61.049 1.00 37.23 S ATOM 10781 SG CYS E 120 41.531 71.815 58.684 1.00 38.33 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 338 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 338 " occ=0.50 Time building chain proxies: 3.81, per 1000 atoms: 0.26 Number of scatterers: 14834 At special positions: 0 Unit cell: (92.4, 124.08, 152.24, 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 2714 8.00 N 2409 7.00 C 9608 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 767.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " Number of angles added : 9 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 15 sheets defined 52.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 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 107 through 111 removed outlier: 3.954A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 111' Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.622A 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 219 through 228 removed outlier: 3.547A pdb=" N HIS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) 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 335 through 339 removed outlier: 3.533A pdb=" N MET A 339 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 4.026A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.744A pdb=" N MET A 384 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 401 through 409 removed outlier: 3.640A pdb=" N ALA A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.947A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.510A pdb=" N PHE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.584A pdb=" N ALA B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.668A pdb=" N LYS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.653A 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 removed outlier: 3.711A pdb=" N THR B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.719A pdb=" N GLN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.666A pdb=" N LEU B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.725A pdb=" N ALA B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 removed outlier: 4.123A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.937A 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 325 removed outlier: 3.720A pdb=" N PHE B 323 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.549A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.948A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.801A pdb=" N ILE B 386 " --> pdb=" O MET B 382 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.813A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 33 Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.983A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 8 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.987A 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 70 through 94 removed outlier: 3.879A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 107 removed outlier: 3.554A pdb=" N SER D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.888A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.860A 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 Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.778A pdb=" N GLY D 172 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 4.398A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.595A pdb=" N SER E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 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 101 Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.509A 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 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 29 removed outlier: 3.552A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.764A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 106 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.595A pdb=" N PHE F 128 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 158 removed outlier: 3.729A pdb=" N GLU F 158 " --> pdb=" O PRO F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 155 through 158' Processing helix chain 'F' and resid 185 through 195 removed outlier: 4.858A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 199 Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.704A 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 354 through 363 Processing helix chain 'F' and resid 380 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.469A pdb=" N ILE A 149 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N CYS A 192 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 151 " --> pdb=" O CYS A 192 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 148 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE A 239 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 150 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 8.238A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.746A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 94 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.284A 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: 7.208A 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: 4.250A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 135 through 138 removed outlier: 6.473A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 141 through 143 Processing sheet with id=AA9, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 108 removed outlier: 7.249A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 208 through 213 removed outlier: 3.821A pdb=" N PHE F 264 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN F 169 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 153 " --> pdb=" O THR F 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB6, first strand: chain 'F' and resid 333 through 336 removed outlier: 6.588A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET F 377 " --> pdb=" O ASP F 404 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2001 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 4840 1.37 - 1.58: 10163 1.58 - 1.78: 11 1.78 - 1.99: 151 1.99 - 2.20: 8 Bond restraints: 15173 Sorted by residual: bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.536 1.407 0.129 1.42e-02 4.96e+03 8.19e+01 bond pdb=" C4A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.288 1.448 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C10 RBF B 502 " pdb=" N1 RBF B 502 " ideal model delta sigma weight residual 1.304 1.461 -0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C5A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.350 1.490 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" CA SER C 228 " pdb=" CB SER C 228 " ideal model delta sigma weight residual 1.532 1.427 0.106 1.53e-02 4.27e+03 4.79e+01 ... (remaining 15168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 20342 3.74 - 7.48: 190 7.48 - 11.23: 22 11.23 - 14.97: 13 14.97 - 18.71: 3 Bond angle restraints: 20570 Sorted by residual: angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.77 13.56 1.14e+00 7.69e-01 1.42e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 89.19 -13.53 1.14e+00 7.69e-01 1.41e+02 angle pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " pdb="FE2 FES D 301 " ideal model delta sigma weight residual 75.66 88.71 -13.05 1.14e+00 7.69e-01 1.31e+02 angle pdb=" S1 FES D 301 " pdb="FE2 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 91.28 13.05 1.14e+00 7.69e-01 1.31e+02 angle pdb="FE1 FES F 501 " pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 89.26 -13.60 1.20e+00 6.94e-01 1.28e+02 ... (remaining 20565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 8683 35.92 - 71.84: 159 71.84 - 107.76: 9 107.76 - 143.68: 2 143.68 - 179.60: 3 Dihedral angle restraints: 8856 sinusoidal: 3490 harmonic: 5366 Sorted by residual: dihedral pdb=" CA HIS A 215 " pdb=" C HIS A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 127.01 52.99 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" C THR C 227 " pdb=" N THR C 227 " pdb=" CA THR C 227 " pdb=" CB THR C 227 " ideal model delta harmonic sigma weight residual -122.00 -100.80 -21.20 0 2.50e+00 1.60e-01 7.19e+01 dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual 257.59 78.00 179.60 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 8853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2244 0.113 - 0.226: 70 0.226 - 0.339: 4 0.339 - 0.452: 3 0.452 - 0.565: 2 Chirality restraints: 2323 Sorted by residual: chirality pdb=" CA THR B 236 " pdb=" N THR B 236 " pdb=" C THR B 236 " pdb=" CB THR B 236 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.97e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.19e+00 chirality pdb=" CA PRO C 174 " pdb=" N PRO C 174 " pdb=" C PRO C 174 " pdb=" CB PRO C 174 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 2320 not shown) Planarity restraints: 2571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.050 2.00e-02 2.50e+03 2.04e-02 1.98e+01 pdb=" C10 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.023 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.016 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.000 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " -0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.053 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 215 " 0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO A 216 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 232 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C TYR B 232 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR B 232 " 0.020 2.00e-02 2.50e+03 pdb=" N SER B 233 " 0.018 2.00e-02 2.50e+03 ... (remaining 2568 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 322 2.69 - 3.24: 14209 3.24 - 3.80: 22254 3.80 - 4.35: 31035 4.35 - 4.90: 52159 Nonbonded interactions: 119979 Sorted by model distance: nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.139 3.040 nonbonded pdb=" O4' FMN B 501 " pdb=" O5' FMN B 501 " model vdw 2.191 2.432 nonbonded pdb=" O GLN F 295 " pdb=" OG SER F 301 " model vdw 2.211 3.040 nonbonded pdb=" ND2 ASN F 140 " pdb=" O LEU F 252 " model vdw 2.223 3.120 nonbonded pdb=" O3' RBF B 502 " pdb=" O5' RBF B 502 " model vdw 2.223 3.040 ... (remaining 119974 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=0.50 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: 2.930 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 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 : 0.017 1.149 15181 Z= 0.528 Angle : 1.055 37.769 20579 Z= 0.565 Chirality : 0.051 0.565 2323 Planarity : 0.005 0.094 2571 Dihedral : 14.813 179.595 5434 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 0.45 % Allowed : 4.28 % Favored : 95.27 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 1885 helix: -0.73 (0.16), residues: 860 sheet: -1.52 (0.38), residues: 177 loop : -2.19 (0.17), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.016 0.001 TYR C 167 PHE 0.045 0.001 PHE B 213 TRP 0.026 0.002 TRP C 146 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.39 (15173) covalent geometry : angle 0.94732 / 0.56 (20570) hydrogen bonds : bond 0.16085 / 11.25 ( 702) hydrogen bonds : angle 6.25187 / 4.51 ( 2001) metal coordination : bond 0.78549 / 45.72 ( 6) metal coordination : angle 22.18978 / 11.30 ( 9) Misc. bond : bond 0.04483 / 2.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 245 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 444 LYS cc_start: 0.7468 (ttmm) cc_final: 0.7095 (tmmt) REVERT: B 367 MET cc_start: 0.8399 (mmm) cc_final: 0.7886 (mmm) REVERT: C 207 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8562 (ttpt) REVERT: C 252 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7636 (mtm110) REVERT: E 151 MET cc_start: 0.7995 (ttp) cc_final: 0.7741 (ttp) REVERT: E 197 GLN cc_start: 0.7891 (pt0) cc_final: 0.7453 (mm-40) REVERT: F 105 GLU cc_start: 0.4882 (mt-10) cc_final: 0.4031 (tt0) REVERT: F 133 TRP cc_start: 0.6882 (m100) cc_final: 0.5755 (m100) REVERT: F 178 LYS cc_start: 0.6804 (mtmm) cc_final: 0.6449 (tptp) REVERT: F 312 ARG cc_start: 0.6469 (mtp-110) cc_final: 0.6162 (ttm-80) outliers start: 7 outliers final: 4 residues processed: 252 average time/residue: 0.1262 time to fit residues: 47.2061 Evaluate side-chains 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 PRO Chi-restraints excluded: chain C residue 207 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 HIS A 225 HIS A 259 GLN B 74 ASN B 219 GLN B 240 GLN B 243 GLN B 252 ASN C 37 GLN C 216 HIS D 56 ASN D 88 GLN D 171 ASN D 176 GLN E 79 ASN F 175 HIS F 176 HIS F 216 ASN F 330 ASN F 347 ASN F 356 HIS F 367 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.173154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133981 restraints weight = 32563.251| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.26 r_work: 0.3273 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15181 Z= 0.164 Angle : 0.592 18.481 20579 Z= 0.298 Chirality : 0.044 0.297 2323 Planarity : 0.005 0.110 2571 Dihedral : 11.078 178.869 2139 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.91 % Allowed : 9.40 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 1885 helix: 0.36 (0.17), residues: 879 sheet: -1.12 (0.37), residues: 177 loop : -1.63 (0.18), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 46 TYR 0.015 0.001 TYR F 217 PHE 0.016 0.001 PHE B 213 TRP 0.024 0.001 TRP B 103 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (15173) covalent geometry : angle 0.56026 / 0.30 (20570) hydrogen bonds : bond 0.05213 / 3.45 ( 702) hydrogen bonds : angle 4.96918 / 3.59 ( 2001) metal coordination : bond 0.01097 / 0.58 ( 6) metal coordination : angle 9.18176 / 5.41 ( 9) Misc. bond : bond 0.00085 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.7628 (ttmm) cc_final: 0.7121 (tmmt) REVERT: B 212 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8744 (mp) REVERT: C 252 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7755 (mtm110) REVERT: E 151 MET cc_start: 0.8627 (ttp) cc_final: 0.8380 (ttp) REVERT: E 197 GLN cc_start: 0.8255 (pt0) cc_final: 0.7490 (mm-40) REVERT: F 105 GLU cc_start: 0.5152 (mt-10) cc_final: 0.4411 (tt0) REVERT: F 133 TRP cc_start: 0.7444 (m100) cc_final: 0.6657 (m100) REVERT: F 178 LYS cc_start: 0.6900 (mtmm) cc_final: 0.6292 (tptp) REVERT: F 312 ARG cc_start: 0.6639 (mtp-110) cc_final: 0.6214 (ttm-80) outliers start: 14 outliers final: 10 residues processed: 202 average time/residue: 0.1217 time to fit residues: 37.0703 Evaluate side-chains 190 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 55 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 GLN B 78 GLN F 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.169594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129367 restraints weight = 31622.233| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.91 r_work: 0.3158 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15181 Z= 0.272 Angle : 0.668 16.830 20579 Z= 0.338 Chirality : 0.048 0.324 2323 Planarity : 0.006 0.126 2571 Dihedral : 10.944 176.617 2129 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.75 % Allowed : 10.83 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 1885 helix: 0.45 (0.17), residues: 878 sheet: -1.04 (0.38), residues: 165 loop : -1.48 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 46 TYR 0.018 0.002 TYR F 319 PHE 0.023 0.002 PHE B 213 TRP 0.025 0.002 TRP B 103 HIS 0.008 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.27 (15173) covalent geometry : angle 0.64840 / 0.34 (20570) hydrogen bonds : bond 0.06146 / 4.04 ( 702) hydrogen bonds : angle 5.04131 / 3.64 ( 2001) metal coordination : bond 0.01225 / 0.81 ( 6) metal coordination : angle 7.79018 / 4.52 ( 9) Misc. bond : bond 0.00190 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8564 (ttm110) cc_final: 0.8251 (ttm110) REVERT: A 444 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7148 (ttpt) REVERT: B 367 MET cc_start: 0.9006 (mmm) cc_final: 0.8569 (mmm) REVERT: C 252 ARG cc_start: 0.8042 (ttm110) cc_final: 0.7446 (mtm110) REVERT: E 151 MET cc_start: 0.8854 (ttp) cc_final: 0.8634 (ttp) REVERT: E 197 GLN cc_start: 0.8463 (pt0) cc_final: 0.7519 (mm-40) REVERT: F 133 TRP cc_start: 0.7458 (m100) cc_final: 0.6636 (m100) REVERT: F 178 LYS cc_start: 0.6885 (mtmm) cc_final: 0.6390 (tptp) REVERT: F 312 ARG cc_start: 0.6640 (mtp-110) cc_final: 0.6243 (ttm-80) outliers start: 27 outliers final: 23 residues processed: 189 average time/residue: 0.1240 time to fit residues: 35.4214 Evaluate side-chains 190 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 chunk 180 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 101 optimal weight: 1.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.178908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.139611 restraints weight = 33333.508| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.07 r_work: 0.3337 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15181 Z= 0.102 Angle : 0.499 11.933 20579 Z= 0.256 Chirality : 0.041 0.254 2323 Planarity : 0.004 0.099 2571 Dihedral : 9.937 177.269 2129 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.30 % Allowed : 11.93 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1885 helix: 1.15 (0.18), residues: 877 sheet: -0.83 (0.38), residues: 177 loop : -1.22 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 46 TYR 0.009 0.001 TYR D 141 PHE 0.015 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (15173) covalent geometry : angle 0.48539 / 0.26 (20570) hydrogen bonds : bond 0.04040 / 2.69 ( 702) hydrogen bonds : angle 4.60360 / 3.32 ( 2001) metal coordination : bond 0.00779 / 0.55 ( 6) metal coordination : angle 5.56010 / 3.26 ( 9) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8306 (ttm110) cc_final: 0.8054 (ttm110) REVERT: A 444 LYS cc_start: 0.7553 (ttmm) cc_final: 0.7007 (tmmt) REVERT: B 367 MET cc_start: 0.8917 (mmm) cc_final: 0.8530 (mmm) REVERT: C 252 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7622 (mtm110) REVERT: E 151 MET cc_start: 0.8538 (ttp) cc_final: 0.8249 (ttp) REVERT: E 197 GLN cc_start: 0.8302 (pt0) cc_final: 0.7538 (mm-40) REVERT: F 133 TRP cc_start: 0.7394 (m100) cc_final: 0.6701 (m100) REVERT: F 178 LYS cc_start: 0.6770 (mtmm) cc_final: 0.6311 (tptp) REVERT: F 312 ARG cc_start: 0.6632 (mtp-110) cc_final: 0.6241 (ttm-80) REVERT: F 347 ASN cc_start: 0.7992 (t0) cc_final: 0.7613 (t0) outliers start: 20 outliers final: 10 residues processed: 206 average time/residue: 0.1233 time to fit residues: 38.1096 Evaluate side-chains 186 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 164 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.173414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132651 restraints weight = 27435.839| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.35 r_work: 0.3288 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15181 Z= 0.153 Angle : 0.551 12.214 20579 Z= 0.279 Chirality : 0.043 0.327 2323 Planarity : 0.005 0.121 2571 Dihedral : 9.583 175.328 2127 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.62 % Allowed : 12.65 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 1885 helix: 1.20 (0.18), residues: 876 sheet: -0.75 (0.39), residues: 177 loop : -1.11 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 289 TYR 0.011 0.001 TYR B 360 PHE 0.020 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (15173) covalent geometry : angle 0.53730 / 0.28 (20570) hydrogen bonds : bond 0.04770 / 3.16 ( 702) hydrogen bonds : angle 4.63668 / 3.34 ( 2001) metal coordination : bond 0.00641 / 0.44 ( 6) metal coordination : angle 5.81191 / 3.35 ( 9) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8047 (ttm110) REVERT: A 444 LYS cc_start: 0.7515 (ttmm) cc_final: 0.7014 (tmmt) REVERT: B 367 MET cc_start: 0.8871 (mmm) cc_final: 0.8466 (mmm) REVERT: C 252 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7544 (mtm110) REVERT: D 50 PHE cc_start: 0.7891 (t80) cc_final: 0.6259 (t80) REVERT: E 151 MET cc_start: 0.8510 (ttp) cc_final: 0.8233 (ttp) REVERT: E 197 GLN cc_start: 0.8314 (pt0) cc_final: 0.7561 (mm-40) REVERT: F 102 GLU cc_start: 0.5992 (pm20) cc_final: 0.5606 (mp0) REVERT: F 133 TRP cc_start: 0.7352 (m100) cc_final: 0.6664 (m100) outliers start: 25 outliers final: 18 residues processed: 197 average time/residue: 0.1180 time to fit residues: 35.3464 Evaluate side-chains 197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 185 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 146 optimal weight: 0.0270 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.4842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133836 restraints weight = 37319.362| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 4.23 r_work: 0.3195 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15181 Z= 0.154 Angle : 0.549 11.697 20579 Z= 0.277 Chirality : 0.044 0.357 2323 Planarity : 0.005 0.123 2571 Dihedral : 9.365 175.023 2127 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.69 % Allowed : 13.04 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1885 helix: 1.24 (0.18), residues: 876 sheet: -0.70 (0.39), residues: 177 loop : -1.06 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.011 0.001 TYR B 360 PHE 0.021 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (15173) covalent geometry : angle 0.53729 / 0.28 (20570) hydrogen bonds : bond 0.04732 / 3.12 ( 702) hydrogen bonds : angle 4.64395 / 3.35 ( 2001) metal coordination : bond 0.00606 / 0.41 ( 6) metal coordination : angle 5.40677 / 3.13 ( 9) Misc. bond : bond 0.00093 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8367 (ttm110) cc_final: 0.8083 (ttm110) REVERT: A 444 LYS cc_start: 0.7456 (ttmm) cc_final: 0.6926 (tmmt) REVERT: B 367 MET cc_start: 0.8901 (mmm) cc_final: 0.8453 (mmm) REVERT: C 252 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7512 (mtm110) REVERT: D 50 PHE cc_start: 0.7861 (t80) cc_final: 0.6240 (t80) REVERT: E 151 MET cc_start: 0.8536 (ttp) cc_final: 0.8261 (ttp) REVERT: E 197 GLN cc_start: 0.8375 (pt0) cc_final: 0.7574 (mm-40) REVERT: F 133 TRP cc_start: 0.7324 (m100) cc_final: 0.6587 (m100) REVERT: F 347 ASN cc_start: 0.8187 (t0) cc_final: 0.7774 (t0) outliers start: 26 outliers final: 17 residues processed: 194 average time/residue: 0.1209 time to fit residues: 35.5918 Evaluate side-chains 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 159 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 65 optimal weight: 0.0970 chunk 147 optimal weight: 8.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132345 restraints weight = 29205.179| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.54 r_work: 0.3274 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15181 Z= 0.156 Angle : 0.557 11.522 20579 Z= 0.280 Chirality : 0.043 0.362 2323 Planarity : 0.005 0.129 2571 Dihedral : 9.301 174.915 2127 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.56 % Allowed : 13.75 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1885 helix: 1.24 (0.18), residues: 877 sheet: -0.64 (0.39), residues: 177 loop : -1.02 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.019 0.001 TYR F 248 PHE 0.021 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (15173) covalent geometry : angle 0.54598 / 0.28 (20570) hydrogen bonds : bond 0.04759 / 3.14 ( 702) hydrogen bonds : angle 4.64693 / 3.35 ( 2001) metal coordination : bond 0.00582 / 0.40 ( 6) metal coordination : angle 5.22518 / 3.03 ( 9) Misc. bond : bond 0.00091 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8326 (ttm110) cc_final: 0.8027 (ttm110) REVERT: A 444 LYS cc_start: 0.7439 (ttmm) cc_final: 0.6971 (tmmt) REVERT: B 367 MET cc_start: 0.8868 (mmm) cc_final: 0.8406 (mmm) REVERT: C 252 ARG cc_start: 0.8055 (ttm110) cc_final: 0.7546 (mtm110) REVERT: D 50 PHE cc_start: 0.7824 (t80) cc_final: 0.7422 (t80) REVERT: E 151 MET cc_start: 0.8531 (ttp) cc_final: 0.8231 (ttp) REVERT: E 197 GLN cc_start: 0.8350 (pt0) cc_final: 0.7603 (mm-40) REVERT: F 133 TRP cc_start: 0.7341 (m100) cc_final: 0.6679 (m100) REVERT: F 221 PHE cc_start: 0.7223 (m-80) cc_final: 0.6880 (m-80) REVERT: F 317 MET cc_start: 0.6744 (ptm) cc_final: 0.6229 (ptp) REVERT: F 347 ASN cc_start: 0.8174 (t0) cc_final: 0.7768 (t0) outliers start: 24 outliers final: 21 residues processed: 194 average time/residue: 0.1217 time to fit residues: 35.9310 Evaluate side-chains 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.178292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137844 restraints weight = 24598.469| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.95 r_work: 0.3375 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15181 Z= 0.111 Angle : 0.510 9.650 20579 Z= 0.259 Chirality : 0.042 0.366 2323 Planarity : 0.005 0.125 2571 Dihedral : 8.966 175.131 2127 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.17 % Allowed : 14.33 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.19), residues: 1885 helix: 1.49 (0.18), residues: 877 sheet: -0.47 (0.40), residues: 177 loop : -0.94 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 108 TYR 0.017 0.001 TYR F 248 PHE 0.018 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15173) covalent geometry : angle 0.50145 / 0.26 (20570) hydrogen bonds : bond 0.04057 / 2.68 ( 702) hydrogen bonds : angle 4.51690 / 3.25 ( 2001) metal coordination : bond 0.00506 / 0.36 ( 6) metal coordination : angle 4.52206 / 2.65 ( 9) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.8352 (ttm110) cc_final: 0.8065 (ttm110) REVERT: A 444 LYS cc_start: 0.7404 (ttmm) cc_final: 0.6871 (tmmt) REVERT: B 367 MET cc_start: 0.8962 (mmm) cc_final: 0.8566 (mmm) REVERT: C 252 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7655 (mtm110) REVERT: E 151 MET cc_start: 0.8607 (ttp) cc_final: 0.8329 (ttp) REVERT: E 197 GLN cc_start: 0.8408 (pt0) cc_final: 0.7543 (mm-40) REVERT: F 6 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8022 (t80) REVERT: F 98 ILE cc_start: 0.6218 (mm) cc_final: 0.5783 (tp) REVERT: F 133 TRP cc_start: 0.7323 (m100) cc_final: 0.6649 (m100) REVERT: F 221 PHE cc_start: 0.7308 (m-80) cc_final: 0.6987 (m-80) REVERT: F 317 MET cc_start: 0.6816 (ptm) cc_final: 0.6240 (ptp) REVERT: F 347 ASN cc_start: 0.8175 (t0) cc_final: 0.7768 (t0) outliers start: 18 outliers final: 15 residues processed: 201 average time/residue: 0.1190 time to fit residues: 36.6968 Evaluate side-chains 197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 97 HIS F 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.173460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133371 restraints weight = 36177.612| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.76 r_work: 0.3205 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15181 Z= 0.163 Angle : 0.570 11.672 20579 Z= 0.285 Chirality : 0.044 0.340 2323 Planarity : 0.005 0.135 2571 Dihedral : 9.089 174.727 2127 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.30 % Allowed : 14.98 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 1885 helix: 1.35 (0.18), residues: 877 sheet: -0.49 (0.40), residues: 177 loop : -0.95 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 289 TYR 0.014 0.001 TYR F 248 PHE 0.024 0.001 PHE F 293 TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 (15173) covalent geometry : angle 0.56068 / 0.28 (20570) hydrogen bonds : bond 0.04784 / 3.15 ( 702) hydrogen bonds : angle 4.61065 / 3.32 ( 2001) metal coordination : bond 0.00615 / 0.39 ( 6) metal coordination : angle 5.03927 / 2.89 ( 9) Misc. bond : bond 0.00093 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.7359 (ttmm) cc_final: 0.6850 (tmmt) REVERT: B 123 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8448 (tt) REVERT: B 367 MET cc_start: 0.8899 (mmm) cc_final: 0.8475 (mmm) REVERT: C 252 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7579 (mtm110) REVERT: D 50 PHE cc_start: 0.7783 (t80) cc_final: 0.7428 (t80) REVERT: E 151 MET cc_start: 0.8534 (ttp) cc_final: 0.8231 (ttp) REVERT: E 197 GLN cc_start: 0.8369 (pt0) cc_final: 0.7549 (mm-40) REVERT: F 6 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8046 (t80) REVERT: F 98 ILE cc_start: 0.6182 (mm) cc_final: 0.4942 (tt) REVERT: F 125 GLU cc_start: 0.6975 (tp30) cc_final: 0.6634 (tp30) REVERT: F 133 TRP cc_start: 0.7346 (m100) cc_final: 0.6615 (m100) REVERT: F 221 PHE cc_start: 0.7333 (m-80) cc_final: 0.6998 (m-80) REVERT: F 317 MET cc_start: 0.6711 (ptm) cc_final: 0.6166 (ptp) REVERT: F 347 ASN cc_start: 0.8181 (t0) cc_final: 0.7778 (t0) outliers start: 20 outliers final: 14 residues processed: 193 average time/residue: 0.1208 time to fit residues: 35.3609 Evaluate side-chains 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135451 restraints weight = 28703.844| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.47 r_work: 0.3319 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15181 Z= 0.139 Angle : 0.552 11.087 20579 Z= 0.276 Chirality : 0.043 0.397 2323 Planarity : 0.005 0.132 2571 Dihedral : 9.002 175.031 2127 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.17 % Allowed : 14.92 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.19), residues: 1885 helix: 1.39 (0.18), residues: 879 sheet: -0.45 (0.40), residues: 177 loop : -0.91 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 289 TYR 0.013 0.001 TYR F 248 PHE 0.020 0.001 PHE F 293 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (15173) covalent geometry : angle 0.54214 / 0.28 (20570) hydrogen bonds : bond 0.04515 / 2.97 ( 702) hydrogen bonds : angle 4.58546 / 3.30 ( 2001) metal coordination : bond 0.00608 / 0.41 ( 6) metal coordination : angle 4.93386 / 2.87 ( 9) Misc. bond : bond 0.00078 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7704 (tpp) cc_final: 0.7278 (tpt) REVERT: A 46 ARG cc_start: 0.8316 (ttm110) cc_final: 0.8059 (mtp85) REVERT: A 444 LYS cc_start: 0.7324 (ttmm) cc_final: 0.6833 (tmmt) REVERT: B 367 MET cc_start: 0.8891 (mmm) cc_final: 0.8458 (mmm) REVERT: C 252 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7650 (mtm110) REVERT: E 151 MET cc_start: 0.8501 (ttp) cc_final: 0.8203 (ttp) REVERT: E 197 GLN cc_start: 0.8314 (pt0) cc_final: 0.7568 (mm-40) REVERT: F 6 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8086 (t80) REVERT: F 98 ILE cc_start: 0.6242 (mm) cc_final: 0.4957 (tt) REVERT: F 125 GLU cc_start: 0.7076 (tp30) cc_final: 0.6742 (tp30) REVERT: F 133 TRP cc_start: 0.7313 (m100) cc_final: 0.6639 (m100) REVERT: F 221 PHE cc_start: 0.7184 (m-80) cc_final: 0.6823 (m-80) REVERT: F 317 MET cc_start: 0.6668 (ptm) cc_final: 0.6167 (ptp) REVERT: F 347 ASN cc_start: 0.8190 (t0) cc_final: 0.7789 (t0) outliers start: 18 outliers final: 15 residues processed: 188 average time/residue: 0.1166 time to fit residues: 33.3199 Evaluate side-chains 190 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 0.0070 chunk 149 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132813 restraints weight = 24666.102| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.98 r_work: 0.3306 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15181 Z= 0.179 Angle : 0.591 12.250 20579 Z= 0.295 Chirality : 0.044 0.388 2323 Planarity : 0.005 0.138 2571 Dihedral : 9.123 174.799 2127 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.43 % Allowed : 14.66 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1885 helix: 1.31 (0.18), residues: 873 sheet: -0.52 (0.39), residues: 177 loop : -0.94 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 289 TYR 0.019 0.002 TYR F 248 PHE 0.021 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (15173) covalent geometry : angle 0.58087 / 0.29 (20570) hydrogen bonds : bond 0.04998 / 3.29 ( 702) hydrogen bonds : angle 4.66358 / 3.36 ( 2001) metal coordination : bond 0.00621 / 0.41 ( 6) metal coordination : angle 5.17068 / 2.96 ( 9) Misc. bond : bond 0.00118 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.03 seconds wall clock time: 66 minutes 32.76 seconds (3992.76 seconds total)