Starting phenix.real_space_refine on Wed Mar 4 20:08:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk6_33245/03_2026/7xk6_33245.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk6_33245/03_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_33245/03_2026/7xk6_33245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk6_33245/03_2026/7xk6_33245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xk6_33245/03_2026/7xk6_33245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk6_33245/03_2026/7xk6_33245.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 Unresolved non-hydrogen dihedrals: 1 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 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 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: 3.68, per 1000 atoms: 0.24 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: 1.37 Conformation dependent library (CDL) restraints added in 818.8 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: 0.50 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: 2.63 Time building geometry restraints manager: 1.80 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: 20534 3.36 - 6.71: 314 6.71 - 10.07: 36 10.07 - 13.43: 14 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 - 35.37: 8941 35.37 - 70.74: 219 70.74 - 106.10: 16 106.10 - 141.47: 8 141.47 - 176.84: 5 Dihedral angle restraints: 9189 sinusoidal: 3754 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 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2216 0.104 - 0.208: 112 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: 2614 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 " -0.065 2.00e-02 2.50e+03 2.87e-02 3.71e+01 pdb=" C10 FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " 0.025 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " -0.024 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " -0.022 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " 0.015 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " 0.031 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " 0.027 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " 0.028 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " -0.010 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " -0.013 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " 0.007 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " -0.025 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " 0.066 2.00e-02 2.50e+03 ... (remaining 2611 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: 3.010 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.360 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 0.015 0.768 15430 Z= 0.529 Angle : 1.129 47.205 20909 Z= 0.610 Chirality : 0.056 0.519 2349 Planarity : 0.008 0.236 2614 Dihedral : 16.136 176.838 5723 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 covalent geometry : bond 0.00755 (15423) covalent geometry : angle 1.01445 (20902) hydrogen bonds : bond 0.20322 ( 701) hydrogen bonds : angle 7.10331 ( 2016) metal coordination : bond 0.68946 ( 5) metal coordination : angle 27.06436 ( 7) Misc. bond : bond 0.04161 ( 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 : 0.591 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: 0.6328 time to fit residues: 146.4516 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 : 0.355 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.096968 restraints weight = 37133.770| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.34 r_work: 0.2966 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 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 = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15430 Z= 0.138 Angle : 0.652 35.124 20909 Z= 0.301 Chirality : 0.043 0.168 2349 Planarity : 0.005 0.116 2614 Dihedral : 13.207 154.800 2373 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.47 % Allowed : 9.48 % 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: -1.11 (0.18), residues: 1910 helix: 0.29 (0.18), residues: 854 sheet: -0.77 (0.39), residues: 160 loop : -1.76 (0.18), residues: 896 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 0.016 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00311 (15423) covalent geometry : angle 0.56560 (20902) hydrogen bonds : bond 0.05209 ( 701) hydrogen bonds : angle 4.93544 ( 2016) metal coordination : bond 0.02505 ( 5) metal coordination : angle 17.70089 ( 7) Misc. bond : bond 0.00062 ( 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 179 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.515 Fit side-chains REVERT: A 75 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7480 (tttt) REVERT: A 396 ASP cc_start: 0.8530 (m-30) cc_final: 0.8236 (m-30) REVERT: A 404 SER cc_start: 0.8918 (t) cc_final: 0.8578 (m) REVERT: B 107 MET cc_start: 0.8887 (ttm) cc_final: 0.8591 (ttm) REVERT: B 151 ARG cc_start: 0.7936 (mmm160) cc_final: 0.6206 (mpt180) REVERT: B 380 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8910 (tt0) REVERT: C 110 GLN cc_start: 0.8602 (mt0) cc_final: 0.8210 (mt0) REVERT: C 116 GLN cc_start: 0.7758 (mt0) cc_final: 0.7458 (mt0) REVERT: C 129 ASP cc_start: 0.7253 (t0) cc_final: 0.6272 (p0) REVERT: D 68 ASN cc_start: 0.7366 (m-40) cc_final: 0.6670 (t0) REVERT: D 96 ASP cc_start: 0.7836 (m-30) cc_final: 0.7604 (m-30) REVERT: D 204 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: D 210 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5700 (tp30) REVERT: E 101 PHE cc_start: 0.7196 (m-80) cc_final: 0.6876 (m-80) REVERT: F 126 GLU cc_start: 0.6712 (mp0) cc_final: 0.6507 (mp0) REVERT: F 200 TYR cc_start: 0.7008 (m-80) cc_final: 0.6762 (m-80) outliers start: 23 outliers final: 4 residues processed: 169 average time/residue: 0.6266 time to fit residues: 115.6849 Evaluate side-chains 145 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 368 ASN B 251 ASN D 18 ASN F 343 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095979 restraints weight = 28264.628| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.71 r_work: 0.2955 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15430 Z= 0.217 Angle : 0.707 39.417 20909 Z= 0.328 Chirality : 0.047 0.176 2349 Planarity : 0.005 0.110 2614 Dihedral : 11.621 152.025 2365 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.56 % Allowed : 10.24 % Favored : 87.20 % 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: -0.74 (0.18), residues: 1910 helix: 0.64 (0.18), residues: 861 sheet: -0.73 (0.40), residues: 162 loop : -1.60 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 43 TYR 0.020 0.002 TYR D 141 PHE 0.023 0.002 PHE B 213 TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00530 (15423) covalent geometry : angle 0.62192 (20902) hydrogen bonds : bond 0.06053 ( 701) hydrogen bonds : angle 4.81544 ( 2016) metal coordination : bond 0.02911 ( 5) metal coordination : angle 18.37276 ( 7) Misc. bond : bond 0.00171 ( 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 179 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.429 Fit side-chains REVERT: A 75 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7245 (tttt) REVERT: A 171 SER cc_start: 0.7431 (OUTLIER) cc_final: 0.7107 (m) REVERT: A 404 SER cc_start: 0.8708 (t) cc_final: 0.8306 (m) REVERT: B 43 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7448 (mtm-85) REVERT: B 107 MET cc_start: 0.8818 (ttm) cc_final: 0.8547 (ttm) REVERT: B 151 ARG cc_start: 0.7907 (mmm160) cc_final: 0.6080 (mpt180) REVERT: C 95 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7203 (mtpm) REVERT: C 129 ASP cc_start: 0.7288 (t0) cc_final: 0.6306 (p0) REVERT: D 49 MET cc_start: 0.8273 (mtp) cc_final: 0.7946 (mtm) REVERT: D 68 ASN cc_start: 0.7421 (m-40) cc_final: 0.6601 (t0) REVERT: D 119 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: D 210 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5676 (tp30) REVERT: E 33 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8266 (mttm) REVERT: F 119 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6911 (mmm) REVERT: F 126 GLU cc_start: 0.6709 (mp0) cc_final: 0.6379 (mp0) REVERT: F 200 TYR cc_start: 0.6930 (m-80) cc_final: 0.6670 (m-80) REVERT: F 244 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8267 (pt0) outliers start: 40 outliers final: 14 residues processed: 164 average time/residue: 0.6014 time to fit residues: 108.2937 Evaluate side-chains 154 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 95 LYS 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 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 119 MET Chi-restraints excluded: chain F residue 203 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 132 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3433 r_free = 0.3433 target = 0.124098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097771 restraints weight = 22377.025| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.59 r_work: 0.2983 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15430 Z= 0.172 Angle : 0.633 33.317 20909 Z= 0.300 Chirality : 0.044 0.165 2349 Planarity : 0.005 0.103 2614 Dihedral : 10.432 143.377 2365 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.50 % Allowed : 11.52 % Favored : 85.98 % 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: -0.43 (0.19), residues: 1910 helix: 0.92 (0.18), residues: 861 sheet: -0.66 (0.40), residues: 162 loop : -1.44 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 43 TYR 0.017 0.001 TYR D 141 PHE 0.020 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00420 (15423) covalent geometry : angle 0.56760 (20902) hydrogen bonds : bond 0.05326 ( 701) hydrogen bonds : angle 4.62669 ( 2016) metal coordination : bond 0.02222 ( 5) metal coordination : angle 15.36196 ( 7) Misc. bond : bond 0.00084 ( 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 182 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.535 Fit side-chains REVERT: A 75 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7203 (tttt) REVERT: A 171 SER cc_start: 0.7372 (OUTLIER) cc_final: 0.7080 (m) REVERT: A 396 ASP cc_start: 0.8391 (m-30) cc_final: 0.8056 (m-30) REVERT: A 404 SER cc_start: 0.8691 (t) cc_final: 0.8312 (m) REVERT: B 5 LYS cc_start: 0.7165 (tmmt) cc_final: 0.6837 (tttp) REVERT: B 43 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7332 (mtm-85) REVERT: B 107 MET cc_start: 0.8830 (ttm) cc_final: 0.8522 (ttm) REVERT: B 151 ARG cc_start: 0.7906 (mmm160) cc_final: 0.6015 (mpt180) REVERT: B 153 HIS cc_start: 0.7410 (m90) cc_final: 0.7200 (m90) REVERT: B 409 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 129 ASP cc_start: 0.7347 (t0) cc_final: 0.6417 (p0) REVERT: D 49 MET cc_start: 0.8234 (mtp) cc_final: 0.7896 (mtm) REVERT: D 68 ASN cc_start: 0.7342 (m-40) cc_final: 0.6572 (t0) REVERT: D 119 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: D 210 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5673 (tp30) REVERT: E 15 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8009 (pt0) REVERT: E 33 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8278 (mttm) REVERT: F 119 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6885 (mmm) REVERT: F 126 GLU cc_start: 0.6513 (mp0) cc_final: 0.6297 (mp0) REVERT: F 200 TYR cc_start: 0.6954 (m-80) cc_final: 0.6688 (m-80) REVERT: F 244 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: F 312 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8010 (mtp180) outliers start: 39 outliers final: 14 residues processed: 171 average time/residue: 0.5909 time to fit residues: 111.0845 Evaluate side-chains 158 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 355 SER Chi-restraints excluded: chain B residue 409 LEU 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 F residue 98 ILE Chi-restraints excluded: chain F residue 119 MET 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 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: 6.9990 chunk 85 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 0.0040 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 176 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 overall best weight: 1.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3466 r_free = 0.3466 target = 0.126606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.097324 restraints weight = 32557.248| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.13 r_work: 0.2984 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1697 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= 0.114 Angle : 0.548 26.019 20909 Z= 0.267 Chirality : 0.042 0.157 2349 Planarity : 0.005 0.124 2614 Dihedral : 9.476 136.423 2362 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.18 % Allowed : 12.87 % Favored : 84.96 % 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: -0.02 (0.19), residues: 1910 helix: 1.28 (0.18), residues: 858 sheet: -0.57 (0.40), residues: 167 loop : -1.22 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.013 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 A 215 Details of bonding type rmsd covalent geometry : bond 0.00261 (15423) covalent geometry : angle 0.50428 (20902) hydrogen bonds : bond 0.04394 ( 701) hydrogen bonds : angle 4.40383 ( 2016) metal coordination : bond 0.01781 ( 5) metal coordination : angle 11.77967 ( 7) Misc. bond : bond 0.00040 ( 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 183 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.568 Fit side-chains REVERT: A 75 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7449 (tttt) REVERT: A 171 SER cc_start: 0.7521 (OUTLIER) cc_final: 0.7254 (m) REVERT: A 396 ASP cc_start: 0.8491 (m-30) cc_final: 0.8199 (m-30) REVERT: A 404 SER cc_start: 0.8796 (t) cc_final: 0.8472 (m) REVERT: B 5 LYS cc_start: 0.7377 (tmmt) cc_final: 0.7047 (tttp) REVERT: B 107 MET cc_start: 0.8941 (ttm) cc_final: 0.8653 (ttm) REVERT: B 151 ARG cc_start: 0.7974 (mmm160) cc_final: 0.6214 (mpt180) REVERT: B 152 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7639 (mttt) REVERT: B 380 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: B 409 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8697 (mt) REVERT: C 129 ASP cc_start: 0.7427 (t0) cc_final: 0.6478 (p0) REVERT: D 49 MET cc_start: 0.8496 (mtp) cc_final: 0.8171 (mtm) REVERT: D 68 ASN cc_start: 0.7541 (m-40) cc_final: 0.6843 (t0) REVERT: D 119 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: D 210 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5757 (tp30) REVERT: E 15 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8145 (pt0) REVERT: F 126 GLU cc_start: 0.6549 (mp0) cc_final: 0.6315 (mp0) REVERT: F 200 TYR cc_start: 0.6984 (m-80) cc_final: 0.6744 (m-80) outliers start: 34 outliers final: 16 residues processed: 172 average time/residue: 0.5526 time to fit residues: 105.1247 Evaluate side-chains 164 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 152 LYS 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 B residue 409 LEU Chi-restraints excluded: chain C residue 123 VAL 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 F residue 38 SER 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 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: 0.0170 chunk 41 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 29 optimal weight: 0.0050 chunk 118 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.9634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099427 restraints weight = 29359.665| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.88 r_work: 0.3002 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15430 Z= 0.112 Angle : 0.536 24.902 20909 Z= 0.262 Chirality : 0.041 0.158 2349 Planarity : 0.005 0.116 2614 Dihedral : 9.180 133.178 2362 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.11 % Allowed : 13.83 % Favored : 84.06 % 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: 0.18 (0.19), residues: 1910 helix: 1.41 (0.18), residues: 860 sheet: -0.50 (0.39), residues: 178 loop : -1.06 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 63 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 0.004 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00258 (15423) covalent geometry : angle 0.49566 (20902) hydrogen bonds : bond 0.04293 ( 701) hydrogen bonds : angle 4.32034 ( 2016) metal coordination : bond 0.01670 ( 5) metal coordination : angle 11.13547 ( 7) Misc. bond : bond 0.00033 ( 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 181 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.528 Fit side-chains REVERT: A 39 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7539 (tmm) REVERT: A 75 LYS cc_start: 0.7927 (ttmm) cc_final: 0.7174 (pttt) REVERT: A 396 ASP cc_start: 0.8362 (m-30) cc_final: 0.8027 (m-30) REVERT: A 404 SER cc_start: 0.8632 (t) cc_final: 0.8256 (m) REVERT: B 5 LYS cc_start: 0.7264 (tmmt) cc_final: 0.6911 (tttp) REVERT: B 107 MET cc_start: 0.8807 (ttm) cc_final: 0.8546 (ttm) REVERT: B 151 ARG cc_start: 0.7802 (mmm160) cc_final: 0.5900 (mpt180) REVERT: B 153 HIS cc_start: 0.7212 (m90) cc_final: 0.6998 (m90) REVERT: B 380 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: C 129 ASP cc_start: 0.7372 (t0) cc_final: 0.6334 (p0) REVERT: D 49 MET cc_start: 0.8218 (mtp) cc_final: 0.7877 (mtm) REVERT: D 68 ASN cc_start: 0.7529 (m-40) cc_final: 0.6788 (t0) REVERT: D 119 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: E 15 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8084 (pt0) REVERT: F 119 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6750 (mmm) REVERT: F 200 TYR cc_start: 0.6859 (m-80) cc_final: 0.6622 (m-80) outliers start: 33 outliers final: 20 residues processed: 168 average time/residue: 0.5716 time to fit residues: 105.5099 Evaluate side-chains 163 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 108 ASN 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 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 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: 3.9990 chunk 70 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.092544 restraints weight = 42440.707| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.53 r_work: 0.2891 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 15430 Z= 0.268 Angle : 0.713 33.519 20909 Z= 0.341 Chirality : 0.048 0.195 2349 Planarity : 0.006 0.137 2614 Dihedral : 9.893 137.925 2362 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.75 % Allowed : 13.64 % 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: -0.26 (0.19), residues: 1910 helix: 0.97 (0.18), residues: 866 sheet: -0.60 (0.40), residues: 164 loop : -1.25 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 43 TYR 0.021 0.002 TYR D 141 PHE 0.025 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 covalent geometry : bond 0.00670 (15423) covalent geometry : angle 0.65437 (20902) hydrogen bonds : bond 0.06324 ( 701) hydrogen bonds : angle 4.68318 ( 2016) metal coordination : bond 0.01965 ( 5) metal coordination : angle 15.55042 ( 7) Misc. bond : bond 0.00145 ( 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 177 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.455 Fit side-chains REVERT: A 39 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.7650 (tmm) REVERT: A 75 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7513 (tttt) REVERT: A 171 SER cc_start: 0.7672 (OUTLIER) cc_final: 0.7441 (m) REVERT: A 404 SER cc_start: 0.8910 (t) cc_final: 0.8597 (m) REVERT: B 5 LYS cc_start: 0.7303 (tmmt) cc_final: 0.6945 (tttp) REVERT: B 43 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7647 (mtm-85) REVERT: B 107 MET cc_start: 0.8970 (ttm) cc_final: 0.8681 (ttm) REVERT: B 151 ARG cc_start: 0.8124 (mmm160) cc_final: 0.6320 (mpt180) REVERT: B 380 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.7651 (tp30) REVERT: B 409 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8964 (mt) REVERT: C 95 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7451 (mtpm) REVERT: C 129 ASP cc_start: 0.7511 (t0) cc_final: 0.6674 (p0) REVERT: D 49 MET cc_start: 0.8514 (mtp) cc_final: 0.8212 (mtm) REVERT: D 68 ASN cc_start: 0.7743 (m-40) cc_final: 0.7059 (t0) REVERT: D 96 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7549 (p0) REVERT: D 119 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: E 33 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8381 (mttm) REVERT: F 119 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6855 (mmt) REVERT: F 200 TYR cc_start: 0.7001 (m-80) cc_final: 0.6760 (m-80) REVERT: F 244 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: F 312 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8314 (mtp180) outliers start: 43 outliers final: 21 residues processed: 164 average time/residue: 0.6070 time to fit residues: 109.1890 Evaluate side-chains 166 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET 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 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 B residue 409 LEU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 69 SER 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 312 ARG 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: 0.8980 chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN F 356 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095853 restraints weight = 35943.299| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.24 r_work: 0.2950 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15430 Z= 0.148 Angle : 0.589 26.469 20909 Z= 0.287 Chirality : 0.043 0.159 2349 Planarity : 0.005 0.128 2614 Dihedral : 9.406 134.097 2359 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 14.92 % Favored : 82.97 % 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: -0.04 (0.19), residues: 1910 helix: 1.18 (0.18), residues: 866 sheet: -0.61 (0.40), residues: 167 loop : -1.14 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 43 TYR 0.017 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 C 199 Details of bonding type rmsd covalent geometry : bond 0.00359 (15423) covalent geometry : angle 0.54491 (20902) hydrogen bonds : bond 0.04994 ( 701) hydrogen bonds : angle 4.48017 ( 2016) metal coordination : bond 0.01973 ( 5) metal coordination : angle 12.24067 ( 7) Misc. bond : bond 0.00053 ( 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: 33 poor density : 137 time to evaluate : 0.467 Fit side-chains REVERT: A 39 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.7625 (tmm) REVERT: A 75 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7459 (tttt) REVERT: A 396 ASP cc_start: 0.8530 (m-30) cc_final: 0.8234 (m-30) REVERT: A 404 SER cc_start: 0.8773 (t) cc_final: 0.8550 (m) REVERT: B 5 LYS cc_start: 0.7400 (tmmt) cc_final: 0.7029 (tttp) REVERT: B 107 MET cc_start: 0.8946 (ttm) cc_final: 0.8710 (ttm) REVERT: B 151 ARG cc_start: 0.8075 (mmm160) cc_final: 0.6268 (mpt180) REVERT: B 380 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: B 409 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8797 (mt) REVERT: C 46 GLN cc_start: 0.8339 (mt0) cc_final: 0.7877 (mt0) REVERT: C 110 GLN cc_start: 0.8451 (mt0) cc_final: 0.8170 (mt0) REVERT: C 116 GLN cc_start: 0.7744 (mt0) cc_final: 0.7403 (mt0) REVERT: D 49 MET cc_start: 0.8506 (mtp) cc_final: 0.8184 (mtm) REVERT: D 68 ASN cc_start: 0.7762 (m-40) cc_final: 0.7061 (t0) REVERT: D 96 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7517 (p0) REVERT: D 119 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: E 33 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8360 (mttm) REVERT: F 119 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6927 (mmm) REVERT: F 200 TYR cc_start: 0.6955 (m-80) cc_final: 0.6726 (m-80) REVERT: F 312 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8144 (mtp180) outliers start: 33 outliers final: 19 residues processed: 162 average time/residue: 0.6272 time to fit residues: 110.8530 Evaluate side-chains 163 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 108 ASN 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 B residue 409 LEU 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 181 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3445 r_free = 0.3445 target = 0.124969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098400 restraints weight = 23714.632| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.66 r_work: 0.2990 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.64 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 = 0.48 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1842 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= 0.144 Angle : 0.580 25.285 20909 Z= 0.284 Chirality : 0.043 0.160 2349 Planarity : 0.005 0.125 2614 Dihedral : 9.209 132.321 2359 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.92 % Allowed : 15.30 % Favored : 82.78 % 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: 0.07 (0.19), residues: 1910 helix: 1.27 (0.18), residues: 867 sheet: -0.57 (0.40), residues: 167 loop : -1.08 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 63 TYR 0.017 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 C 199 Details of bonding type rmsd covalent geometry : bond 0.00347 (15423) covalent geometry : angle 0.53853 (20902) hydrogen bonds : bond 0.04893 ( 701) hydrogen bonds : angle 4.43728 ( 2016) metal coordination : bond 0.01884 ( 5) metal coordination : angle 11.71259 ( 7) Misc. bond : bond 0.00054 ( 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 166 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.523 Fit side-chains REVERT: A 39 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.7519 (tmm) REVERT: A 75 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7199 (tttt) REVERT: A 171 SER cc_start: 0.7380 (OUTLIER) cc_final: 0.7129 (m) REVERT: A 396 ASP cc_start: 0.8368 (m-30) cc_final: 0.8053 (m-30) REVERT: A 404 SER cc_start: 0.8539 (t) cc_final: 0.8278 (m) REVERT: B 5 LYS cc_start: 0.7301 (tmmt) cc_final: 0.6919 (tttp) REVERT: B 107 MET cc_start: 0.8838 (ttm) cc_final: 0.8524 (ttm) REVERT: B 151 ARG cc_start: 0.7943 (mmm160) cc_final: 0.6088 (mpt180) REVERT: B 380 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: B 409 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8626 (mt) REVERT: C 46 GLN cc_start: 0.8182 (mt0) cc_final: 0.7657 (mt0) REVERT: C 110 GLN cc_start: 0.8309 (mt0) cc_final: 0.8014 (mt0) REVERT: C 116 GLN cc_start: 0.7602 (mt0) cc_final: 0.7235 (mt0) REVERT: D 49 MET cc_start: 0.8255 (mtp) cc_final: 0.7908 (mtm) REVERT: D 68 ASN cc_start: 0.7690 (m-40) cc_final: 0.6916 (t0) REVERT: D 96 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7294 (p0) REVERT: D 119 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: E 33 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8268 (mttm) REVERT: F 119 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6733 (mmm) REVERT: F 200 TYR cc_start: 0.7005 (m-80) cc_final: 0.6758 (m-80) REVERT: F 312 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8006 (mtp180) outliers start: 30 outliers final: 20 residues processed: 159 average time/residue: 0.6179 time to fit residues: 107.7276 Evaluate side-chains 161 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET 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 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 B residue 409 LEU 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 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 203 LYS Chi-restraints excluded: chain F residue 208 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 157 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3432 r_free = 0.3432 target = 0.123942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.094714 restraints weight = 40891.957| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.52 r_work: 0.2918 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15430 Z= 0.179 Angle : 0.616 26.491 20909 Z= 0.300 Chirality : 0.044 0.163 2349 Planarity : 0.005 0.124 2614 Dihedral : 9.298 132.828 2359 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.05 % Allowed : 15.36 % Favored : 82.59 % 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: -0.01 (0.19), residues: 1910 helix: 1.19 (0.18), residues: 868 sheet: -0.58 (0.41), residues: 167 loop : -1.11 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 43 TYR 0.019 0.001 TYR D 141 PHE 0.021 0.002 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00441 (15423) covalent geometry : angle 0.57258 (20902) hydrogen bonds : bond 0.05321 ( 701) hydrogen bonds : angle 4.49957 ( 2016) metal coordination : bond 0.01902 ( 5) metal coordination : angle 12.49247 ( 7) Misc. bond : bond 0.00088 ( 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 164 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.569 Fit side-chains REVERT: A 39 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.7642 (tmm) REVERT: A 75 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7508 (tttt) REVERT: A 171 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7356 (m) REVERT: A 404 SER cc_start: 0.8778 (t) cc_final: 0.8529 (m) REVERT: B 5 LYS cc_start: 0.7406 (tmmt) cc_final: 0.7014 (tttp) REVERT: B 107 MET cc_start: 0.8970 (ttm) cc_final: 0.8732 (ttm) REVERT: B 151 ARG cc_start: 0.8050 (mmm160) cc_final: 0.6338 (mpt180) REVERT: B 380 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: B 409 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8853 (mt) REVERT: C 46 GLN cc_start: 0.8357 (mt0) cc_final: 0.7867 (mt0) REVERT: C 110 GLN cc_start: 0.8458 (mt0) cc_final: 0.8187 (mt0) REVERT: C 116 GLN cc_start: 0.7807 (mt0) cc_final: 0.7465 (mt0) REVERT: D 49 MET cc_start: 0.8508 (mtp) cc_final: 0.8193 (mtm) REVERT: D 68 ASN cc_start: 0.7824 (m-40) cc_final: 0.7065 (t0) REVERT: D 96 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7608 (p0) REVERT: D 119 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: E 33 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8387 (mttm) REVERT: F 119 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6927 (mmm) REVERT: F 200 TYR cc_start: 0.7117 (m-80) cc_final: 0.6886 (m-80) REVERT: F 312 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7891 (ttp-170) outliers start: 32 outliers final: 21 residues processed: 157 average time/residue: 0.6190 time to fit residues: 106.5729 Evaluate side-chains 161 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET 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 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 B residue 409 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 25 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 176 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 177 VAL Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 208 ILE 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 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: 0.0870 chunk 45 optimal weight: 0.0060 chunk 127 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3478 r_free = 0.3478 target = 0.127639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098776 restraints weight = 35699.459| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.25 r_work: 0.2994 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 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 = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15430 Z= 0.104 Angle : 0.527 20.638 20909 Z= 0.263 Chirality : 0.041 0.154 2349 Planarity : 0.005 0.118 2614 Dihedral : 8.736 127.646 2359 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.41 % Allowed : 16.01 % Favored : 82.59 % 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: 0.34 (0.19), residues: 1910 helix: 1.50 (0.18), residues: 861 sheet: -0.44 (0.39), residues: 178 loop : -0.93 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 63 TYR 0.013 0.001 TYR D 141 PHE 0.015 0.001 PHE B 6 TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00235 (15423) covalent geometry : angle 0.49665 (20902) hydrogen bonds : bond 0.04080 ( 701) hydrogen bonds : angle 4.29118 ( 2016) metal coordination : bond 0.01754 ( 5) metal coordination : angle 9.66857 ( 7) Misc. bond : bond 0.00016 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5127.77 seconds wall clock time: 87 minutes 55.09 seconds (5275.09 seconds total)