Starting phenix.real_space_refine on Fri Jul 3 20:31:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xk6_33245/07_2026/7xk6_33245.cif" } resolution = 3.0 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= 0.004 sd= 0.111 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 9778 2.51 5 N 2448 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 15123 Number of models: 1 Model: "" Number of chains: 16 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: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3173 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 396} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1558 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1507 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 221 Unusual residues: {'0NI': 1, 'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8663 SG CYS D 29 45.569 69.551 91.992 1.00 50.25 S ATOM 10264 SG CYS E 26 43.772 72.562 87.829 1.00 51.15 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: 4.40, per 1000 atoms: 0.29 Number of scatterers: 15123 At special positions: 0 Unit cell: (91.52, 126.72, 155.76, 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 2794 8.00 N 2448 7.00 C 9778 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: 1.45 Conformation dependent library (CDL) restraints added in 670.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 111 " Number of angles added : 7 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3466 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 12 sheets defined 52.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 109 through 113 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: 3.934A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.629A pdb=" N THR A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.931A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.526A pdb=" N ILE B 10 " --> pdb=" O PHE B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.952A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.756A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.784A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.513A pdb=" N LEU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.703A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.711A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.559A pdb=" N LYS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.559A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 236 through 239 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.562A 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: 3.665A pdb=" N ALA B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.632A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.511A pdb=" N PHE B 323 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 324' Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.048A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 353 through 374 removed outlier: 4.031A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.949A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.593A pdb=" N ASP B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.530A pdb=" N VAL C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 4.163A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.149A pdb=" N GLN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.656A pdb=" N ASN C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.835A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) 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 35 removed outlier: 3.788A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.522A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.534A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.686A pdb=" N ILE D 108 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.045A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.719A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.762A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 4.539A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 removed outlier: 3.623A pdb=" N VAL D 206 " --> pdb=" O PRO D 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 206' Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.679A pdb=" N LEU E 7 " --> pdb=" O HIS E 3 " (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 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 removed outlier: 3.927A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.961A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 removed outlier: 3.567A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 188 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 244 through 252 removed outlier: 3.516A pdb=" N TRP F 250 " --> pdb=" O SER F 246 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 252 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.915A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 328 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 removed outlier: 3.623A pdb=" N CYS F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 393 removed outlier: 3.573A pdb=" N ALA F 385 " --> pdb=" O PRO F 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.393A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.543A pdb=" N LEU A 274 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 307 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.567A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 74 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.181A 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: 4.022A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 15.057A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.505A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR C 150 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 154 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 164 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU C 156 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 162 " --> pdb=" O GLU C 156 " (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 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 37 through 38 removed outlier: 6.062A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU F 122 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE F 83 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 208 through 213 removed outlier: 3.506A pdb=" N ILE F 208 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 260 " --> pdb=" O TRP F 133 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.391A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 339 " --> pdb=" O TYR F 351 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 701 hydrogen bonds defined for protein. 2016 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: 2.25 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: 1.16 - 1.37: 4890 1.37 - 1.58: 10363 1.58 - 1.78: 14 1.78 - 1.99: 148 1.99 - 2.20: 8 Bond restraints: 15423 Sorted by residual: bond pdb=" C4A RBF B 601 " pdb=" N5 RBF B 601 " ideal model delta sigma weight residual 1.288 1.447 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" C10 RBF B 601 " pdb=" N1 RBF B 601 " ideal model delta sigma weight residual 1.304 1.460 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" C5A RBF B 601 " pdb=" N5 RBF B 601 " ideal model delta sigma weight residual 1.350 1.488 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.528 1.436 0.092 1.34e-02 5.57e+03 4.73e+01 bond pdb=" C PRO B 217 " pdb=" O PRO B 217 " ideal model delta sigma weight residual 1.235 1.163 0.071 1.11e-02 8.12e+03 4.11e+01 ... (remaining 15418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 20532 3.36 - 6.71: 315 6.71 - 10.07: 39 10.07 - 13.43: 12 13.43 - 16.79: 4 Bond angle restraints: 20902 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 90.64 13.69 1.14e+00 7.69e-01 1.44e+02 angle pdb=" S1 FES F 501 " pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.63 13.70 1.20e+00 6.94e-01 1.30e+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 88.59 -12.93 1.14e+00 7.69e-01 1.29e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 91.46 12.87 1.14e+00 7.69e-01 1.27e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 88.37 -12.71 1.14e+00 7.69e-01 1.24e+02 ... (remaining 20897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8800 35.47 - 70.94: 188 70.94 - 106.41: 16 106.41 - 141.87: 3 141.87 - 177.34: 2 Dihedral angle restraints: 9009 sinusoidal: 3574 harmonic: 5435 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 180.00 121.90 58.10 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SER F 99 " pdb=" C SER F 99 " pdb=" N LYS F 100 " pdb=" CA LYS F 100 " ideal model delta harmonic sigma weight residual 180.00 -127.22 -52.78 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA GLN D 24 " pdb=" C GLN D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta harmonic sigma weight residual -180.00 -142.93 -37.07 0 5.00e+00 4.00e-02 5.50e+01 ... (remaining 9006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2217 0.104 - 0.208: 111 0.208 - 0.312: 14 0.312 - 0.415: 3 0.415 - 0.519: 4 Chirality restraints: 2349 Sorted by residual: 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 2.20 0.52 2.00e-01 2.50e+01 6.74e+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 2.13 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA PRO B 379 " pdb=" N PRO B 379 " pdb=" C PRO B 379 " pdb=" CB PRO B 379 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.92e+00 ... (remaining 2346 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 0NI B 602 " 0.280 2.00e-02 2.50e+03 2.36e-01 6.98e+02 pdb=" C16 0NI B 602 " -0.398 2.00e-02 2.50e+03 pdb=" C17 0NI B 602 " -0.089 2.00e-02 2.50e+03 pdb=" C18 0NI B 602 " 0.022 2.00e-02 2.50e+03 pdb=" C19 0NI B 602 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0NI B 602 " -0.073 2.00e-02 2.50e+03 6.13e-02 4.70e+01 pdb=" C11 0NI B 602 " 0.097 2.00e-02 2.50e+03 pdb=" C12 0NI B 602 " 0.025 2.00e-02 2.50e+03 pdb=" C13 0NI B 602 " 0.010 2.00e-02 2.50e+03 pdb=" C14 0NI B 602 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " -0.069 2.00e-02 2.50e+03 2.83e-02 3.82e+01 pdb=" C10 FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " 0.027 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " -0.016 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " 0.033 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " 0.026 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " 0.025 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " 0.067 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " -0.017 2.00e-02 2.50e+03 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 270 2.68 - 3.24: 14042 3.24 - 3.79: 22083 3.79 - 4.35: 32122 4.35 - 4.90: 53627 Nonbonded interactions: 122144 Sorted by model distance: nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.129 3.040 nonbonded pdb=" NH1 ARG F 80 " pdb=" OE1 GLU F 107 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR B 87 " pdb=" O ASP B 230 " model vdw 2.207 3.040 nonbonded pdb=" O LEU F 95 " pdb=" OG SER F 99 " model vdw 2.221 3.040 nonbonded pdb=" O4' FMN B 600 " pdb=" O5' FMN B 600 " model vdw 2.225 2.432 ... (remaining 122139 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.280 Find NCS groups from input model: 0.100 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:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 : 0.014 0.768 15430 Z= 0.526 Angle : 1.128 47.205 20909 Z= 0.610 Chirality : 0.057 0.519 2349 Planarity : 0.008 0.236 2612 Dihedral : 15.008 177.342 5543 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.36 % Favored : 96.33 % Rotamer: Outliers : 0.70 % Allowed : 2.94 % Favored : 96.35 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.16 % 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: -2.57 (0.16), residues: 1910 helix: -1.08 (0.16), residues: 835 sheet: -1.38 (0.37), residues: 168 loop : -2.36 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.041 0.002 TYR B 412 PHE 0.034 0.002 PHE B 213 TRP 0.023 0.002 TRP C 146 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.44 (15423) covalent geometry : angle 1.01375 / 0.61 (20902) hydrogen bonds : bond 0.20322 / 13.61 ( 701) hydrogen bonds : angle 7.10331 / 5.09 ( 2016) metal coordination : bond 0.68946 / 39.17 ( 5) metal coordination : angle 27.06436 / 12.97 ( 7) Misc. bond : bond 0.04161 / 2.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.425 Fit side-chains REVERT: A 75 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7158 (tttt) REVERT: A 396 ASP cc_start: 0.8098 (m-30) cc_final: 0.7774 (m-30) REVERT: A 404 SER cc_start: 0.8884 (t) cc_final: 0.8581 (m) REVERT: B 9 ASP cc_start: 0.7221 (m-30) cc_final: 0.7003 (m-30) REVERT: B 151 ARG cc_start: 0.7890 (mmm160) cc_final: 0.6415 (mpt180) REVERT: C 110 GLN cc_start: 0.8493 (mt0) cc_final: 0.8035 (mt0) REVERT: C 116 GLN cc_start: 0.7774 (mt0) cc_final: 0.7556 (mt0) REVERT: C 129 ASP cc_start: 0.7253 (t0) cc_final: 0.6302 (p0) REVERT: D 68 ASN cc_start: 0.7505 (m110) cc_final: 0.6989 (t0) REVERT: D 96 ASP cc_start: 0.7205 (m-30) cc_final: 0.6949 (m-30) REVERT: D 210 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5798 (tp30) REVERT: E 10 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7836 (ttmm) REVERT: E 15 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7677 (pt0) REVERT: E 101 PHE cc_start: 0.7390 (m-80) cc_final: 0.7039 (m-80) REVERT: F 126 GLU cc_start: 0.6407 (mp0) cc_final: 0.6166 (mp0) REVERT: F 200 TYR cc_start: 0.6778 (m-80) cc_final: 0.6500 (m-80) REVERT: F 383 MET cc_start: 0.7800 (ttp) cc_final: 0.7592 (ttp) outliers start: 11 outliers final: 5 residues processed: 212 average time/residue: 0.5657 time to fit residues: 131.2429 Evaluate side-chains 146 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 174 PRO Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN A 88 GLN A 109 GLN A 215 HIS B 74 ASN B 78 GLN B 156 ASN B 178 GLN B 219 GLN B 243 GLN B 354 ASN B 404 ASN C 37 GLN C 46 GLN C 120 ASN C 160 ASN D 18 ASN D 24 GLN D 68 ASN D 75 GLN D 88 GLN D 100 GLN D 205 GLN E 79 ASN E 107 ASN F 78 GLN F 140 ASN F 176 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.097381 restraints weight = 37201.444| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.33 r_work: 0.2964 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15430 Z= 0.137 Angle : 0.656 36.342 20909 Z= 0.300 Chirality : 0.043 0.184 2349 Planarity : 0.005 0.116 2612 Dihedral : 11.203 178.876 2193 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.54 % Allowed : 9.41 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.18), residues: 1910 helix: 0.30 (0.18), residues: 854 sheet: -0.87 (0.38), residues: 165 loop : -1.74 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 210 TYR 0.014 0.001 TYR D 141 PHE 0.015 0.001 PHE C 235 TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15423) covalent geometry : angle 0.56219 / 0.30 (20902) hydrogen bonds : bond 0.05154 / 3.45 ( 701) hydrogen bonds : angle 4.93759 / 3.55 ( 2016) metal coordination : bond 0.02381 / 1.35 ( 5) metal coordination : angle 18.50647 / 9.29 ( 7) Misc. bond : bond 0.00112 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.588 Fit side-chains REVERT: A 75 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7478 (tttt) REVERT: A 396 ASP cc_start: 0.8534 (m-30) cc_final: 0.8238 (m-30) REVERT: A 404 SER cc_start: 0.8916 (t) cc_final: 0.8580 (m) REVERT: B 107 MET cc_start: 0.8893 (ttm) cc_final: 0.8604 (ttm) REVERT: B 151 ARG cc_start: 0.7939 (mmm160) cc_final: 0.6209 (mpt180) REVERT: B 380 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8918 (tt0) REVERT: C 110 GLN cc_start: 0.8600 (mt0) cc_final: 0.8211 (mt0) REVERT: C 116 GLN cc_start: 0.7764 (mt0) cc_final: 0.7462 (mt0) REVERT: C 129 ASP cc_start: 0.7246 (t0) cc_final: 0.6268 (p0) REVERT: D 68 ASN cc_start: 0.7380 (m-40) cc_final: 0.6686 (t0) REVERT: D 96 ASP cc_start: 0.7834 (m-30) cc_final: 0.7621 (m-30) REVERT: D 204 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: D 210 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5711 (tp30) REVERT: E 101 PHE cc_start: 0.7188 (m-80) cc_final: 0.6865 (m-80) REVERT: F 126 GLU cc_start: 0.6716 (mp0) cc_final: 0.6509 (mp0) REVERT: F 200 TYR cc_start: 0.7004 (m-80) cc_final: 0.6756 (m-80) outliers start: 24 outliers final: 4 residues processed: 170 average time/residue: 0.5695 time to fit residues: 106.0126 Evaluate side-chains 146 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 171 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 chunk 5 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN B 251 ASN F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099011 restraints weight = 28072.292| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.84 r_work: 0.2998 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15430 Z= 0.130 Angle : 0.594 32.009 20909 Z= 0.280 Chirality : 0.043 0.165 2349 Planarity : 0.005 0.105 2612 Dihedral : 10.638 179.416 2185 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.05 % Allowed : 9.86 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % 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: -0.46 (0.19), residues: 1910 helix: 0.89 (0.18), residues: 861 sheet: -0.71 (0.40), residues: 167 loop : -1.45 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 43 TYR 0.015 0.001 TYR D 141 PHE 0.018 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (15423) covalent geometry : angle 0.52685 / 0.28 (20902) hydrogen bonds : bond 0.04807 / 3.22 ( 701) hydrogen bonds : angle 4.59034 / 3.31 ( 2016) metal coordination : bond 0.02703 / 1.35 ( 5) metal coordination : angle 14.95364 / 7.43 ( 7) Misc. bond : bond 0.00111 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.555 Fit side-chains REVERT: A 75 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7204 (tttt) REVERT: A 396 ASP cc_start: 0.8372 (m-30) cc_final: 0.8043 (m-30) REVERT: A 404 SER cc_start: 0.8643 (t) cc_final: 0.8254 (m) REVERT: B 107 MET cc_start: 0.8804 (ttm) cc_final: 0.8511 (ttm) REVERT: B 151 ARG cc_start: 0.7808 (mmm160) cc_final: 0.5985 (mpt180) REVERT: C 129 ASP cc_start: 0.7194 (t0) cc_final: 0.6164 (p0) REVERT: D 49 MET cc_start: 0.8234 (mtp) cc_final: 0.7904 (mtm) REVERT: D 68 ASN cc_start: 0.7297 (m-40) cc_final: 0.6527 (t0) REVERT: D 96 ASP cc_start: 0.7725 (m-30) cc_final: 0.7515 (m-30) REVERT: D 119 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: D 210 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5661 (tp30) REVERT: E 101 PHE cc_start: 0.7064 (m-80) cc_final: 0.6706 (m-80) REVERT: F 126 GLU cc_start: 0.6693 (mp0) cc_final: 0.6410 (mp0) REVERT: F 200 TYR cc_start: 0.6903 (m-80) cc_final: 0.6608 (m-80) outliers start: 32 outliers final: 8 residues processed: 165 average time/residue: 0.5364 time to fit residues: 97.7230 Evaluate side-chains 142 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 132 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.096418 restraints weight = 22574.935| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.55 r_work: 0.2960 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15430 Z= 0.256 Angle : 0.728 38.966 20909 Z= 0.339 Chirality : 0.048 0.181 2349 Planarity : 0.005 0.128 2612 Dihedral : 10.585 179.372 2182 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.43 % Allowed : 11.40 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.16 % 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: -0.54 (0.19), residues: 1910 helix: 0.80 (0.18), residues: 860 sheet: -0.68 (0.40), residues: 162 loop : -1.47 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 81 TYR 0.022 0.002 TYR D 141 PHE 0.024 0.002 PHE B 213 TRP 0.021 0.002 TRP B 103 HIS 0.007 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.26 (15423) covalent geometry : angle 0.64901 / 0.34 (20902) hydrogen bonds : bond 0.06296 / 4.19 ( 701) hydrogen bonds : angle 4.75810 / 3.44 ( 2016) metal coordination : bond 0.02261 / 1.10 ( 5) metal coordination : angle 17.98227 / 8.79 ( 7) Misc. bond : bond 0.00205 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.598 Fit side-chains REVERT: A 75 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7235 (tttt) REVERT: A 171 SER cc_start: 0.7432 (OUTLIER) cc_final: 0.7145 (m) REVERT: A 404 SER cc_start: 0.8715 (t) cc_final: 0.8300 (m) REVERT: B 107 MET cc_start: 0.8835 (ttm) cc_final: 0.8550 (ttm) REVERT: B 151 ARG cc_start: 0.7936 (mmm160) cc_final: 0.6071 (mpt180) REVERT: B 380 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: B 409 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 129 ASP cc_start: 0.7329 (t0) cc_final: 0.6398 (p0) REVERT: D 49 MET cc_start: 0.8269 (mtp) cc_final: 0.7946 (mtm) REVERT: D 68 ASN cc_start: 0.7456 (m-40) cc_final: 0.6694 (t0) REVERT: D 119 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: D 210 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5683 (tp30) REVERT: E 15 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8024 (pt0) REVERT: F 119 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6896 (mmm) REVERT: F 126 GLU cc_start: 0.6685 (mp0) cc_final: 0.6387 (mp0) REVERT: F 200 TYR cc_start: 0.6968 (m-80) cc_final: 0.6687 (m-80) REVERT: F 244 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8322 (pt0) REVERT: F 312 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7983 (mtp180) outliers start: 38 outliers final: 20 residues processed: 161 average time/residue: 0.5406 time to fit residues: 95.8867 Evaluate side-chains 161 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 70 CYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 93 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN F 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098743 restraints weight = 32609.845| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.00 r_work: 0.2987 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15430 Z= 0.109 Angle : 0.549 26.525 20909 Z= 0.267 Chirality : 0.041 0.158 2349 Planarity : 0.005 0.114 2612 Dihedral : 10.003 179.591 2182 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.66 % Allowed : 12.55 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: -0.09 (0.19), residues: 1910 helix: 1.19 (0.18), residues: 867 sheet: -0.58 (0.39), residues: 178 loop : -1.24 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.014 0.001 TYR D 141 PHE 0.015 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15423) covalent geometry : angle 0.50168 / 0.27 (20902) hydrogen bonds : bond 0.04390 / 2.96 ( 701) hydrogen bonds : angle 4.43596 / 3.20 ( 2016) metal coordination : bond 0.01939 / 0.97 ( 5) metal coordination : angle 12.25424 / 6.12 ( 7) Misc. bond : bond 0.00057 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.476 Fit side-chains REVERT: A 75 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7221 (tttt) REVERT: A 396 ASP cc_start: 0.8408 (m-30) cc_final: 0.8089 (m-30) REVERT: A 404 SER cc_start: 0.8682 (t) cc_final: 0.8305 (m) REVERT: B 5 LYS cc_start: 0.7267 (tmmt) cc_final: 0.6946 (tttp) REVERT: B 107 MET cc_start: 0.8808 (ttm) cc_final: 0.8506 (ttm) REVERT: B 151 ARG cc_start: 0.7879 (mmm160) cc_final: 0.5906 (mpt180) REVERT: B 380 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: C 129 ASP cc_start: 0.7309 (t0) cc_final: 0.6371 (p0) REVERT: D 68 ASN cc_start: 0.7349 (m-40) cc_final: 0.6657 (t0) REVERT: D 210 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5627 (tp30) REVERT: E 15 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8049 (pt0) REVERT: F 119 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6903 (mmm) REVERT: F 126 GLU cc_start: 0.6536 (mp0) cc_final: 0.6301 (mp0) REVERT: F 200 TYR cc_start: 0.6911 (m-80) cc_final: 0.6645 (m-80) REVERT: F 244 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8256 (pt0) outliers start: 26 outliers final: 12 residues processed: 169 average time/residue: 0.5347 time to fit residues: 100.2951 Evaluate side-chains 152 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 110 optimal weight: 0.0370 chunk 128 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN D 19 ASN F 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098681 restraints weight = 29422.980| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.87 r_work: 0.2992 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15430 Z= 0.124 Angle : 0.558 27.167 20909 Z= 0.270 Chirality : 0.042 0.162 2349 Planarity : 0.005 0.126 2612 Dihedral : 9.799 179.421 2182 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.92 % Allowed : 13.64 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 0.12 (0.19), residues: 1910 helix: 1.34 (0.18), residues: 866 sheet: -0.52 (0.39), residues: 178 loop : -1.10 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 43 TYR 0.016 0.001 TYR D 141 PHE 0.018 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (15423) covalent geometry : angle 0.51202 / 0.27 (20902) hydrogen bonds : bond 0.04546 / 3.05 ( 701) hydrogen bonds : angle 4.37839 / 3.16 ( 2016) metal coordination : bond 0.01713 / 0.86 ( 5) metal coordination : angle 12.13723 / 5.97 ( 7) Misc. bond : bond 0.00090 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.436 Fit side-chains REVERT: A 75 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7217 (tttt) REVERT: A 171 SER cc_start: 0.7327 (OUTLIER) cc_final: 0.7035 (m) REVERT: A 396 ASP cc_start: 0.8374 (m-30) cc_final: 0.8042 (m-30) REVERT: A 404 SER cc_start: 0.8670 (t) cc_final: 0.8309 (m) REVERT: B 5 LYS cc_start: 0.7296 (tmmt) cc_final: 0.6971 (tttp) REVERT: B 107 MET cc_start: 0.8829 (ttm) cc_final: 0.8544 (ttm) REVERT: B 151 ARG cc_start: 0.7897 (mmm160) cc_final: 0.6029 (mpt180) REVERT: B 380 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: C 129 ASP cc_start: 0.7328 (t0) cc_final: 0.6320 (p0) REVERT: D 68 ASN cc_start: 0.7462 (m-40) cc_final: 0.6770 (t0) REVERT: D 119 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: D 210 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.5701 (tp30) REVERT: F 119 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6763 (mmm) REVERT: F 200 TYR cc_start: 0.6880 (m-80) cc_final: 0.6642 (m-80) REVERT: F 244 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8267 (pt0) outliers start: 30 outliers final: 19 residues processed: 165 average time/residue: 0.5332 time to fit residues: 96.8809 Evaluate side-chains 160 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.092989 restraints weight = 42349.040| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.51 r_work: 0.2901 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15430 Z= 0.232 Angle : 0.682 33.549 20909 Z= 0.325 Chirality : 0.047 0.181 2349 Planarity : 0.005 0.124 2612 Dihedral : 10.140 179.616 2182 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.11 % Allowed : 14.28 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.16 % 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: -0.20 (0.19), residues: 1910 helix: 1.03 (0.18), residues: 867 sheet: -0.66 (0.40), residues: 167 loop : -1.22 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 81 TYR 0.021 0.002 TYR D 141 PHE 0.024 0.002 PHE B 213 TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.23 (15423) covalent geometry : angle 0.62030 / 0.32 (20902) hydrogen bonds : bond 0.06042 / 4.02 ( 701) hydrogen bonds : angle 4.64269 / 3.36 ( 2016) metal coordination : bond 0.01948 / 0.95 ( 5) metal coordination : angle 15.47204 / 7.58 ( 7) Misc. bond : bond 0.00158 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.367 Fit side-chains REVERT: A 39 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.7637 (tmm) REVERT: A 75 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7499 (tttt) REVERT: A 171 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.7397 (m) REVERT: A 404 SER cc_start: 0.8921 (t) cc_final: 0.8572 (m) REVERT: B 5 LYS cc_start: 0.7352 (tmmt) cc_final: 0.6998 (tttp) REVERT: B 107 MET cc_start: 0.8972 (ttm) cc_final: 0.8688 (ttm) REVERT: B 151 ARG cc_start: 0.8121 (mmm160) cc_final: 0.6371 (mpt180) REVERT: B 380 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.7710 (tp30) REVERT: C 44 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: C 129 ASP cc_start: 0.7512 (t0) cc_final: 0.6660 (p0) REVERT: D 49 MET cc_start: 0.8516 (mtp) cc_final: 0.8208 (mtm) REVERT: D 68 ASN cc_start: 0.7745 (m-40) cc_final: 0.7059 (t0) REVERT: D 96 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7572 (p0) REVERT: D 119 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: F 119 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6952 (mmm) REVERT: F 200 TYR cc_start: 0.6998 (m-80) cc_final: 0.6764 (m-80) REVERT: F 244 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8410 (pt0) outliers start: 33 outliers final: 21 residues processed: 155 average time/residue: 0.5565 time to fit residues: 94.9731 Evaluate side-chains 162 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 56 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN B 153 HIS F 356 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.097451 restraints weight = 35874.717| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.26 r_work: 0.2974 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15430 Z= 0.119 Angle : 0.544 24.539 20909 Z= 0.267 Chirality : 0.042 0.156 2349 Planarity : 0.005 0.115 2612 Dihedral : 9.604 179.244 2179 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.92 % Allowed : 14.72 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 0.14 (0.19), residues: 1910 helix: 1.34 (0.18), residues: 866 sheet: -0.56 (0.40), residues: 167 loop : -1.04 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 TYR 0.015 0.001 TYR D 141 PHE 0.016 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (15423) covalent geometry : angle 0.50428 / 0.27 (20902) hydrogen bonds : bond 0.04432 / 2.98 ( 701) hydrogen bonds : angle 4.38529 / 3.17 ( 2016) metal coordination : bond 0.01860 / 0.92 ( 5) metal coordination : angle 11.21998 / 5.55 ( 7) Misc. bond : bond 0.00071 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.592 Fit side-chains REVERT: A 75 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7432 (tttt) REVERT: A 171 SER cc_start: 0.7518 (OUTLIER) cc_final: 0.7253 (m) REVERT: A 396 ASP cc_start: 0.8489 (m-30) cc_final: 0.8190 (m-30) REVERT: A 404 SER cc_start: 0.8800 (t) cc_final: 0.8479 (m) REVERT: B 5 LYS cc_start: 0.7401 (tmmt) cc_final: 0.7037 (tttp) REVERT: B 107 MET cc_start: 0.8932 (ttm) cc_final: 0.8694 (ttm) REVERT: B 151 ARG cc_start: 0.8016 (mmm160) cc_final: 0.6285 (mpt180) REVERT: B 380 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: C 46 GLN cc_start: 0.8343 (mt0) cc_final: 0.7856 (mt0) REVERT: C 110 GLN cc_start: 0.8405 (mt0) cc_final: 0.8131 (mt0) REVERT: C 116 GLN cc_start: 0.7739 (mt0) cc_final: 0.7389 (mt0) REVERT: D 49 MET cc_start: 0.8478 (mtp) cc_final: 0.8149 (mtm) REVERT: D 68 ASN cc_start: 0.7736 (m-40) cc_final: 0.7021 (t0) REVERT: D 96 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7551 (p0) REVERT: F 119 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6932 (mmm) REVERT: F 200 TYR cc_start: 0.6935 (m-80) cc_final: 0.6712 (m-80) REVERT: F 244 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8337 (pt0) outliers start: 30 outliers final: 18 residues processed: 160 average time/residue: 0.5542 time to fit residues: 97.5678 Evaluate side-chains 159 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 181 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.0050 chunk 148 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 45 optimal weight: 0.0270 chunk 101 optimal weight: 1.9990 chunk 55 optimal weight: 0.0060 chunk 145 optimal weight: 5.9990 overall best weight: 0.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN B 153 HIS F 357 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102248 restraints weight = 23562.180| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.66 r_work: 0.3048 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15430 Z= 0.098 Angle : 0.510 21.146 20909 Z= 0.255 Chirality : 0.041 0.155 2349 Planarity : 0.005 0.110 2612 Dihedral : 9.270 179.289 2179 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.79 % Allowed : 15.17 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 0.44 (0.19), residues: 1910 helix: 1.59 (0.18), residues: 864 sheet: -0.43 (0.39), residues: 178 loop : -0.89 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 43 TYR 0.012 0.001 TYR D 141 PHE 0.015 0.001 PHE B 6 TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (15423) covalent geometry : angle 0.47959 / 0.25 (20902) hydrogen bonds : bond 0.03848 / 2.60 ( 701) hydrogen bonds : angle 4.23159 / 3.06 ( 2016) metal coordination : bond 0.01630 / 0.82 ( 5) metal coordination : angle 9.48772 / 4.64 ( 7) Misc. bond : bond 0.00052 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.371 Fit side-chains REVERT: A 75 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7156 (pttt) REVERT: A 171 SER cc_start: 0.7453 (OUTLIER) cc_final: 0.7133 (m) REVERT: A 396 ASP cc_start: 0.8260 (m-30) cc_final: 0.7998 (m-30) REVERT: A 404 SER cc_start: 0.8635 (t) cc_final: 0.8203 (m) REVERT: B 5 LYS cc_start: 0.7295 (tmmt) cc_final: 0.6937 (tttp) REVERT: B 107 MET cc_start: 0.8791 (ttm) cc_final: 0.8525 (ttm) REVERT: B 151 ARG cc_start: 0.7732 (mmm160) cc_final: 0.5954 (mpt180) REVERT: C 110 GLN cc_start: 0.8276 (mt0) cc_final: 0.8002 (mt0) REVERT: C 116 GLN cc_start: 0.7517 (mt0) cc_final: 0.7175 (mt0) REVERT: D 49 MET cc_start: 0.8168 (mtp) cc_final: 0.7798 (mtm) REVERT: D 68 ASN cc_start: 0.7660 (m-40) cc_final: 0.6928 (t0) REVERT: D 96 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7257 (p0) REVERT: D 119 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: F 119 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6654 (mmm) REVERT: F 200 TYR cc_start: 0.6977 (m-80) cc_final: 0.6757 (m-80) outliers start: 28 outliers final: 15 residues processed: 164 average time/residue: 0.5193 time to fit residues: 93.9114 Evaluate side-chains 157 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 157 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 121 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097242 restraints weight = 40512.216| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.50 r_work: 0.2961 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15430 Z= 0.130 Angle : 0.550 24.337 20909 Z= 0.270 Chirality : 0.042 0.160 2349 Planarity : 0.005 0.135 2612 Dihedral : 9.339 178.575 2179 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.34 % Allowed : 15.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 0.38 (0.19), residues: 1910 helix: 1.53 (0.18), residues: 864 sheet: -0.44 (0.39), residues: 178 loop : -0.91 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.014 0.001 TYR D 141 PHE 0.018 0.001 PHE B 6 TRP 0.022 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (15423) covalent geometry : angle 0.51284 / 0.27 (20902) hydrogen bonds : bond 0.04499 / 3.02 ( 701) hydrogen bonds : angle 4.30926 / 3.12 ( 2016) metal coordination : bond 0.01713 / 0.84 ( 5) metal coordination : angle 10.82618 / 5.26 ( 7) Misc. bond : bond 0.00090 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.466 Fit side-chains REVERT: A 75 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7490 (pttt) REVERT: A 171 SER cc_start: 0.7544 (OUTLIER) cc_final: 0.7281 (m) REVERT: A 396 ASP cc_start: 0.8472 (m-30) cc_final: 0.8252 (m-30) REVERT: A 404 SER cc_start: 0.8804 (t) cc_final: 0.8533 (m) REVERT: B 5 LYS cc_start: 0.7410 (tmmt) cc_final: 0.7053 (tttp) REVERT: B 107 MET cc_start: 0.8924 (ttm) cc_final: 0.8692 (ttm) REVERT: B 151 ARG cc_start: 0.7974 (mmm160) cc_final: 0.6229 (mpt180) REVERT: C 46 GLN cc_start: 0.8332 (mt0) cc_final: 0.7776 (mt0) REVERT: C 110 GLN cc_start: 0.8371 (mt0) cc_final: 0.8124 (mt0) REVERT: C 116 GLN cc_start: 0.7654 (mt0) cc_final: 0.7306 (mt0) REVERT: D 49 MET cc_start: 0.8481 (mtp) cc_final: 0.8161 (mtm) REVERT: D 68 ASN cc_start: 0.7754 (m-40) cc_final: 0.7061 (t0) REVERT: D 96 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7543 (p0) REVERT: D 119 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: F 119 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6519 (mmm) REVERT: F 200 TYR cc_start: 0.7073 (m-80) cc_final: 0.6867 (m-80) outliers start: 21 outliers final: 13 residues processed: 150 average time/residue: 0.5500 time to fit residues: 90.8985 Evaluate side-chains 153 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 133 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 127 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097309 restraints weight = 35577.946| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.29 r_work: 0.2966 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15430 Z= 0.134 Angle : 0.557 24.304 20909 Z= 0.273 Chirality : 0.042 0.159 2349 Planarity : 0.005 0.135 2612 Dihedral : 9.373 178.457 2179 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.54 % Allowed : 15.75 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 1910 helix: 1.51 (0.18), residues: 866 sheet: -0.49 (0.40), residues: 167 loop : -0.90 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 43 TYR 0.014 0.001 TYR D 141 PHE 0.017 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (15423) covalent geometry : angle 0.51984 / 0.27 (20902) hydrogen bonds : bond 0.04604 / 3.09 ( 701) hydrogen bonds : angle 4.33344 / 3.14 ( 2016) metal coordination : bond 0.01768 / 0.87 ( 5) metal coordination : angle 11.01306 / 5.39 ( 7) Misc. bond : bond 0.00094 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4490.48 seconds wall clock time: 77 minutes 14.29 seconds (4634.29 seconds total)