Starting phenix.real_space_refine on Wed Mar 4 18:47:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk4_33243/03_2026/7xk4_33243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk4_33243/03_2026/7xk4_33243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xk4_33243/03_2026/7xk4_33243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk4_33243/03_2026/7xk4_33243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xk4_33243/03_2026/7xk4_33243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk4_33243/03_2026/7xk4_33243.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9608 2.51 5 N 2409 2.21 5 O 2714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 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: 14834 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3153 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 194 Unusual residues: {'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10059 SG CYS E 26 44.968 71.154 67.325 1.00 30.11 S ATOM 8454 SG CYS D 29 43.216 68.000 63.365 1.00 31.69 S ATOM 10781 SG CYS E 120 41.788 71.960 60.755 1.00 37.71 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: 3.74, per 1000 atoms: 0.25 Number of scatterers: 14834 At special positions: 0 Unit cell: (90.64, 124.96, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2714 8.00 N 2409 7.00 C 9608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 634.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " Number of angles added : 7 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 14 sheets defined 51.8% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 108 through 113 removed outlier: 4.244A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) 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: 3.878A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 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 removed outlier: 3.640A pdb=" N HIS A 313 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.019A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.707A pdb=" N GLU A 412 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 409 through 413' Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.940A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.965A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.689A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.514A pdb=" N LYS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.131A pdb=" N THR B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.636A pdb=" N GLY B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.597A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 245 removed outlier: 4.089A pdb=" N ALA B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 removed outlier: 4.099A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.970A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 325' Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.500A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 3.722A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.658A pdb=" N ILE B 386 " --> pdb=" O MET B 382 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.755A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.514A pdb=" N THR C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.711A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.256A pdb=" N GLN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'C' and resid 178 through 181 removed outlier: 3.638A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 181' Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.759A 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 19 through 24 Processing helix chain 'D' and resid 27 through 34 removed outlier: 4.036A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.755A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.579A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 108 removed outlier: 4.435A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.788A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.844A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.636A pdb=" N LEU D 182 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 202 removed outlier: 4.335A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.596A pdb=" N SER E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) removed outlier: 3.609A 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 110 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 175 through 191 removed outlier: 3.789A pdb=" N THR E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) 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: 3.976A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 63 Processing helix chain 'F' and resid 91 through 98 Processing helix chain 'F' and resid 99 through 106 removed outlier: 3.649A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 removed outlier: 4.260A pdb=" N PHE F 128 " --> pdb=" O PRO F 124 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 129' Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 188 through 196 removed outlier: 4.156A pdb=" N TRP F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 removed outlier: 3.620A pdb=" N SER F 247 " --> pdb=" O GLY F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 removed outlier: 3.774A pdb=" N PHE F 323 " --> pdb=" O TYR F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 347 removed outlier: 3.733A pdb=" N ASN F 347 " --> pdb=" O PRO F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 removed outlier: 3.785A pdb=" N CYS F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 394 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.179A 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 22 removed outlier: 8.430A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.762A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.970A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 366 through 367 removed outlier: 4.800A pdb=" N LEU B 39 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.587A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.616A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.571A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR C 125 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA9, first strand: chain 'C' and resid 204 through 206 removed outlier: 6.431A pdb=" N LYS C 204 " --> pdb=" O VAL C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'F' and resid 46 through 49 removed outlier: 6.659A pdb=" N THR F 36 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU F 121 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.480A pdb=" N GLN F 169 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE F 224 " --> pdb=" O LEU F 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 176 through 178 Processing sheet with id=AB5, first strand: chain 'F' and resid 335 through 339 removed outlier: 6.292A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.36: 4709 1.36 - 1.57: 10292 1.57 - 1.78: 12 1.78 - 1.99: 152 1.99 - 2.20: 8 Bond restraints: 15173 Sorted by residual: bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.536 1.420 0.116 1.42e-02 4.96e+03 6.69e+01 bond pdb=" C4A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.288 1.450 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C10 RBF B 502 " pdb=" N1 RBF B 502 " ideal model delta sigma weight residual 1.304 1.462 -0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C5A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.350 1.490 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" CA SER C 228 " pdb=" CB SER C 228 " ideal model delta sigma weight residual 1.531 1.423 0.107 1.59e-02 3.96e+03 4.57e+01 ... (remaining 15168 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 20249 3.57 - 7.14: 277 7.14 - 10.71: 29 10.71 - 14.28: 13 14.28 - 17.85: 2 Bond angle restraints: 20570 Sorted by residual: angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.85 13.48 1.14e+00 7.69e-01 1.40e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 89.09 -13.43 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " pdb="FE2 FES D 301 " ideal model delta sigma weight residual 75.66 88.74 -13.08 1.14e+00 7.69e-01 1.32e+02 angle pdb=" S1 FES D 301 " pdb="FE2 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 91.32 13.01 1.14e+00 7.69e-01 1.30e+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 90.85 13.48 1.20e+00 6.94e-01 1.26e+02 ... (remaining 20565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 8799 35.15 - 70.31: 216 70.31 - 105.46: 9 105.46 - 140.62: 10 140.62 - 175.77: 2 Dihedral angle restraints: 9036 sinusoidal: 3670 harmonic: 5366 Sorted by residual: dihedral pdb=" C PRO B 217 " pdb=" N PRO B 217 " pdb=" CA PRO B 217 " pdb=" CB PRO B 217 " ideal model delta harmonic sigma weight residual -120.70 -105.90 -14.80 0 2.50e+00 1.60e-01 3.51e+01 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 -150.59 -29.41 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" C GLU B 274 " pdb=" N GLU B 274 " pdb=" CA GLU B 274 " pdb=" CB GLU B 274 " ideal model delta harmonic sigma weight residual -122.60 -108.09 -14.51 0 2.50e+00 1.60e-01 3.37e+01 ... (remaining 9033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2173 0.095 - 0.189: 124 0.189 - 0.284: 18 0.284 - 0.379: 3 0.379 - 0.473: 5 Chirality restraints: 2323 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 2.25 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA ILE B 272 " pdb=" N ILE B 272 " pdb=" C ILE B 272 " pdb=" CB ILE B 272 " both_signs ideal model delta sigma weight residual False 2.43 2.00 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA THR C 173 " pdb=" N THR C 173 " pdb=" C THR C 173 " pdb=" CB THR C 173 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 2320 not shown) Planarity restraints: 2573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.051 2.00e-02 2.50e+03 2.30e-02 2.38e+01 pdb=" C10 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.020 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.018 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.015 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.013 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.029 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.018 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.020 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " -0.002 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.003 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.018 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 210 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA B 210 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA B 210 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 211 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 167 " 0.018 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C ALA B 167 " -0.058 2.00e-02 2.50e+03 pdb=" O ALA B 167 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 168 " 0.020 2.00e-02 2.50e+03 ... (remaining 2570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 818 2.72 - 3.27: 14302 3.27 - 3.81: 23401 3.81 - 4.36: 29805 4.36 - 4.90: 52105 Nonbonded interactions: 120431 Sorted by model distance: nonbonded pdb=" O SER F 68 " pdb=" NE2 GLN F 169 " model vdw 2.180 3.120 nonbonded pdb=" ND2 ASN C 40 " pdb=" O ALA D 92 " model vdw 2.223 3.120 nonbonded pdb=" O SER A 289 " pdb=" OG SER A 289 " model vdw 2.231 3.040 nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.250 3.040 nonbonded pdb=" O4' FMN B 501 " pdb=" O5' FMN B 501 " model vdw 2.254 2.432 ... (remaining 120426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 14.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.016 1.188 15180 Z= 0.554 Angle : 1.061 35.914 20577 Z= 0.601 Chirality : 0.054 0.473 2323 Planarity : 0.005 0.060 2573 Dihedral : 15.847 175.769 5614 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 0.71 % Allowed : 3.70 % Favored : 95.59 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.17), residues: 1885 helix: -0.80 (0.16), residues: 841 sheet: -1.49 (0.36), residues: 162 loop : -2.20 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 209 TYR 0.018 0.001 TYR F 217 PHE 0.030 0.002 PHE B 213 TRP 0.022 0.002 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00739 (15173) covalent geometry : angle 0.99469 (20570) hydrogen bonds : bond 0.16415 ( 713) hydrogen bonds : angle 6.91877 ( 2076) metal coordination : bond 0.77997 ( 5) metal coordination : angle 20.05003 ( 7) Misc. bond : bond 0.04388 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 0.601 Fit side-chains REVERT: A 77 VAL cc_start: 0.8514 (p) cc_final: 0.8307 (m) REVERT: A 343 ASN cc_start: 0.8055 (m-40) cc_final: 0.7837 (p0) REVERT: B 224 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 172 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: D 44 MET cc_start: 0.8987 (tpt) cc_final: 0.8562 (tpt) REVERT: E 51 ILE cc_start: 0.8541 (mt) cc_final: 0.8333 (mt) REVERT: F 20 LEU cc_start: 0.8003 (mt) cc_final: 0.7786 (mt) outliers start: 11 outliers final: 4 residues processed: 245 average time/residue: 0.1097 time to fit residues: 40.6889 Evaluate side-chains 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 209 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 109 GLN A 215 HIS B 74 ASN B 178 GLN B 219 GLN B 240 GLN B 243 GLN B 313 ASN C 37 GLN C 116 GLN D 88 GLN D 100 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN E 16 ASN F 216 ASN F 227 ASN F 239 ASN F 244 GLN F 295 GLN F 332 ASN F 367 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106537 restraints weight = 31859.260| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.58 r_work: 0.2843 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 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 = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15180 Z= 0.154 Angle : 0.567 11.243 20577 Z= 0.293 Chirality : 0.043 0.195 2323 Planarity : 0.005 0.060 2573 Dihedral : 12.875 168.674 2323 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.23 % Allowed : 8.56 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.18), residues: 1885 helix: 0.47 (0.18), residues: 848 sheet: -0.85 (0.38), residues: 160 loop : -1.63 (0.18), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.017 0.001 TYR F 217 PHE 0.017 0.001 PHE D 50 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00359 (15173) covalent geometry : angle 0.55658 (20570) hydrogen bonds : bond 0.05058 ( 713) hydrogen bonds : angle 5.18877 ( 2076) metal coordination : bond 0.03180 ( 5) metal coordination : angle 5.88077 ( 7) Misc. bond : bond 0.00110 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.507 Fit side-chains REVERT: A 172 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7380 (mp0) REVERT: D 44 MET cc_start: 0.8885 (tpt) cc_final: 0.8482 (tpt) REVERT: D 117 ARG cc_start: 0.8551 (mmp-170) cc_final: 0.8338 (mmp-170) REVERT: F 360 TYR cc_start: 0.8317 (t80) cc_final: 0.7801 (t80) outliers start: 19 outliers final: 11 residues processed: 203 average time/residue: 0.1142 time to fit residues: 35.1148 Evaluate side-chains 191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 55 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN D 65 HIS D 137 ASN E 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.141026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.103566 restraints weight = 31049.335| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.38 r_work: 0.2837 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15180 Z= 0.166 Angle : 0.558 10.008 20577 Z= 0.287 Chirality : 0.043 0.223 2323 Planarity : 0.004 0.055 2573 Dihedral : 11.880 159.479 2314 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.62 % Allowed : 10.05 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1885 helix: 0.99 (0.18), residues: 846 sheet: -0.54 (0.39), residues: 160 loop : -1.42 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.019 0.001 TYR F 248 PHE 0.020 0.001 PHE F 24 TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00400 (15173) covalent geometry : angle 0.55416 (20570) hydrogen bonds : bond 0.04957 ( 713) hydrogen bonds : angle 4.96469 ( 2076) metal coordination : bond 0.00607 ( 5) metal coordination : angle 3.48677 ( 7) Misc. bond : bond 0.00086 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.436 Fit side-chains REVERT: A 124 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7666 (mm-30) REVERT: C 49 ILE cc_start: 0.8413 (mt) cc_final: 0.8195 (mp) REVERT: D 44 MET cc_start: 0.8941 (tpt) cc_final: 0.8518 (tpt) REVERT: F 257 LYS cc_start: 0.7663 (tptt) cc_final: 0.7396 (tptt) REVERT: F 346 ASP cc_start: 0.6989 (m-30) cc_final: 0.6695 (m-30) REVERT: F 360 TYR cc_start: 0.8331 (t80) cc_final: 0.7789 (t80) outliers start: 25 outliers final: 14 residues processed: 204 average time/residue: 0.1050 time to fit residues: 33.0580 Evaluate side-chains 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 180 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 HIS D 65 HIS F 330 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.140388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.103010 restraints weight = 33140.372| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.10 r_work: 0.2765 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15180 Z= 0.187 Angle : 0.563 9.196 20577 Z= 0.291 Chirality : 0.044 0.192 2323 Planarity : 0.004 0.058 2573 Dihedral : 11.542 159.896 2312 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.14 % Allowed : 11.74 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.19), residues: 1885 helix: 1.09 (0.18), residues: 851 sheet: -0.32 (0.40), residues: 158 loop : -1.32 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.021 0.001 TYR F 248 PHE 0.020 0.002 PHE B 213 TRP 0.022 0.002 TRP B 103 HIS 0.007 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00458 (15173) covalent geometry : angle 0.56033 (20570) hydrogen bonds : bond 0.05051 ( 713) hydrogen bonds : angle 4.91691 ( 2076) metal coordination : bond 0.00654 ( 5) metal coordination : angle 3.19529 ( 7) Misc. bond : bond 0.00099 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.551 Fit side-chains REVERT: A 46 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7222 (mtm-85) REVERT: A 124 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 59 MET cc_start: 0.8682 (mmp) cc_final: 0.8181 (mmt) REVERT: D 44 MET cc_start: 0.8945 (tpt) cc_final: 0.8477 (tpt) REVERT: F 257 LYS cc_start: 0.7600 (tptt) cc_final: 0.7271 (tptt) REVERT: F 346 ASP cc_start: 0.7006 (m-30) cc_final: 0.6642 (m-30) REVERT: F 360 TYR cc_start: 0.8202 (t80) cc_final: 0.7709 (t80) outliers start: 33 outliers final: 23 residues processed: 210 average time/residue: 0.1049 time to fit residues: 34.1071 Evaluate side-chains 206 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 164 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 181 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS F 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.141915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104307 restraints weight = 26852.433| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.97 r_work: 0.2861 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15180 Z= 0.149 Angle : 0.526 8.095 20577 Z= 0.274 Chirality : 0.042 0.172 2323 Planarity : 0.004 0.059 2573 Dihedral : 11.201 159.633 2310 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.08 % Allowed : 13.04 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.19), residues: 1885 helix: 1.24 (0.18), residues: 853 sheet: -0.29 (0.40), residues: 160 loop : -1.21 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.021 0.001 TYR F 248 PHE 0.020 0.001 PHE F 24 TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00356 (15173) covalent geometry : angle 0.52354 (20570) hydrogen bonds : bond 0.04649 ( 713) hydrogen bonds : angle 4.81926 ( 2076) metal coordination : bond 0.00516 ( 5) metal coordination : angle 2.98844 ( 7) Misc. bond : bond 0.00073 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.512 Fit side-chains REVERT: A 124 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 197 GLN cc_start: 0.8493 (mt0) cc_final: 0.8246 (mt0) REVERT: F 108 ARG cc_start: 0.6721 (mtm-85) cc_final: 0.6014 (mtp180) REVERT: F 214 MET cc_start: 0.8079 (mtm) cc_final: 0.7860 (mtm) REVERT: F 257 LYS cc_start: 0.7630 (tptt) cc_final: 0.7300 (tptt) REVERT: F 346 ASP cc_start: 0.7008 (m-30) cc_final: 0.6633 (m-30) REVERT: F 360 TYR cc_start: 0.8223 (t80) cc_final: 0.7845 (t80) outliers start: 32 outliers final: 20 residues processed: 209 average time/residue: 0.1019 time to fit residues: 33.2094 Evaluate side-chains 206 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.141170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107109 restraints weight = 36665.239| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.87 r_work: 0.2762 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15180 Z= 0.178 Angle : 0.548 7.307 20577 Z= 0.284 Chirality : 0.043 0.184 2323 Planarity : 0.004 0.059 2573 Dihedral : 11.106 159.613 2310 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 13.88 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1885 helix: 1.25 (0.18), residues: 852 sheet: -0.24 (0.40), residues: 158 loop : -1.16 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 260 TYR 0.024 0.001 TYR F 248 PHE 0.019 0.001 PHE B 213 TRP 0.023 0.002 TRP B 103 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00435 (15173) covalent geometry : angle 0.54553 (20570) hydrogen bonds : bond 0.04888 ( 713) hydrogen bonds : angle 4.84074 ( 2076) metal coordination : bond 0.00640 ( 5) metal coordination : angle 2.94387 ( 7) Misc. bond : bond 0.00091 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.534 Fit side-chains REVERT: A 46 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7232 (mtm-85) REVERT: A 124 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7634 (mm-30) REVERT: E 197 GLN cc_start: 0.8492 (mt0) cc_final: 0.8247 (mt0) REVERT: F 108 ARG cc_start: 0.6635 (mtm-85) cc_final: 0.5953 (mtp180) REVERT: F 214 MET cc_start: 0.8069 (mtm) cc_final: 0.7824 (mtm) REVERT: F 257 LYS cc_start: 0.7561 (tptt) cc_final: 0.7336 (tptt) REVERT: F 346 ASP cc_start: 0.6961 (m-30) cc_final: 0.6570 (m-30) REVERT: F 360 TYR cc_start: 0.8190 (t80) cc_final: 0.7798 (t80) outliers start: 34 outliers final: 30 residues processed: 205 average time/residue: 0.1056 time to fit residues: 33.1059 Evaluate side-chains 211 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS E 92 GLN F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.139160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102560 restraints weight = 28835.506| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.18 r_work: 0.2794 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15180 Z= 0.266 Angle : 0.625 7.407 20577 Z= 0.322 Chirality : 0.047 0.228 2323 Planarity : 0.005 0.058 2573 Dihedral : 11.278 160.342 2310 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 2.40 % Allowed : 14.27 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1885 helix: 1.00 (0.18), residues: 858 sheet: -0.26 (0.41), residues: 158 loop : -1.16 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 260 TYR 0.027 0.002 TYR F 248 PHE 0.023 0.002 PHE F 24 TRP 0.024 0.002 TRP B 103 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00663 (15173) covalent geometry : angle 0.62147 (20570) hydrogen bonds : bond 0.05697 ( 713) hydrogen bonds : angle 4.99901 ( 2076) metal coordination : bond 0.01040 ( 5) metal coordination : angle 3.85382 ( 7) Misc. bond : bond 0.00139 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.577 Fit side-chains REVERT: A 46 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7294 (mtm-85) REVERT: A 124 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 16 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8153 (mp) REVERT: F 108 ARG cc_start: 0.6701 (mtm-85) cc_final: 0.6042 (mtp180) REVERT: F 127 ILE cc_start: 0.8974 (mm) cc_final: 0.8732 (mm) REVERT: F 257 LYS cc_start: 0.7564 (tptt) cc_final: 0.7294 (tptt) REVERT: F 346 ASP cc_start: 0.7017 (m-30) cc_final: 0.6760 (m-30) REVERT: F 360 TYR cc_start: 0.8305 (t80) cc_final: 0.7809 (t80) outliers start: 37 outliers final: 31 residues processed: 209 average time/residue: 0.1063 time to fit residues: 33.9194 Evaluate side-chains 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 131 GLN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.139448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101416 restraints weight = 24808.386| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.87 r_work: 0.2851 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15180 Z= 0.149 Angle : 0.542 12.988 20577 Z= 0.278 Chirality : 0.043 0.181 2323 Planarity : 0.004 0.058 2573 Dihedral : 10.927 159.791 2310 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.14 % Allowed : 14.72 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1885 helix: 1.25 (0.18), residues: 861 sheet: -0.24 (0.40), residues: 160 loop : -1.09 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.025 0.001 TYR F 248 PHE 0.017 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00355 (15173) covalent geometry : angle 0.53243 (20570) hydrogen bonds : bond 0.04687 ( 713) hydrogen bonds : angle 4.82853 ( 2076) metal coordination : bond 0.02159 ( 5) metal coordination : angle 5.59794 ( 7) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.525 Fit side-chains REVERT: A 46 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7372 (mtm-85) REVERT: A 124 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7702 (mm-30) REVERT: F 108 ARG cc_start: 0.6792 (mtm-85) cc_final: 0.6182 (mtp180) REVERT: F 127 ILE cc_start: 0.8974 (mm) cc_final: 0.8772 (mm) REVERT: F 257 LYS cc_start: 0.7647 (tptt) cc_final: 0.7443 (tptt) REVERT: F 346 ASP cc_start: 0.7084 (m-30) cc_final: 0.6802 (m-30) REVERT: F 360 TYR cc_start: 0.8311 (t80) cc_final: 0.7945 (t80) outliers start: 33 outliers final: 26 residues processed: 205 average time/residue: 0.1007 time to fit residues: 31.5730 Evaluate side-chains 209 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 169 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.141041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.106020 restraints weight = 36167.897| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.58 r_work: 0.2734 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15180 Z= 0.125 Angle : 0.518 11.307 20577 Z= 0.266 Chirality : 0.042 0.172 2323 Planarity : 0.004 0.058 2573 Dihedral : 10.669 159.195 2310 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.14 % Allowed : 14.92 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 1885 helix: 1.40 (0.18), residues: 859 sheet: -0.17 (0.40), residues: 165 loop : -1.02 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.024 0.001 TYR F 248 PHE 0.016 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00290 (15173) covalent geometry : angle 0.50986 (20570) hydrogen bonds : bond 0.04351 ( 713) hydrogen bonds : angle 4.73795 ( 2076) metal coordination : bond 0.00745 ( 5) metal coordination : angle 4.98287 ( 7) Misc. bond : bond 0.00048 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.553 Fit side-chains REVERT: A 46 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7330 (mtm-85) REVERT: A 124 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7693 (mm-30) REVERT: D 50 PHE cc_start: 0.7381 (t80) cc_final: 0.6452 (m-10) REVERT: E 197 GLN cc_start: 0.8515 (mt0) cc_final: 0.8300 (mt0) REVERT: F 108 ARG cc_start: 0.6802 (mtm-85) cc_final: 0.6184 (mtp180) REVERT: F 214 MET cc_start: 0.8167 (mtm) cc_final: 0.7948 (mtm) REVERT: F 257 LYS cc_start: 0.7607 (tptt) cc_final: 0.7407 (tptt) REVERT: F 346 ASP cc_start: 0.7008 (m-30) cc_final: 0.6617 (m-30) REVERT: F 360 TYR cc_start: 0.8292 (t80) cc_final: 0.7918 (t80) outliers start: 33 outliers final: 27 residues processed: 206 average time/residue: 0.1092 time to fit residues: 34.5401 Evaluate side-chains 207 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.0060 chunk 115 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 63 optimal weight: 0.0980 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.142760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.106002 restraints weight = 28730.612| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.31 r_work: 0.2855 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15180 Z= 0.099 Angle : 0.490 9.253 20577 Z= 0.253 Chirality : 0.041 0.169 2323 Planarity : 0.004 0.059 2573 Dihedral : 10.301 158.607 2310 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.49 % Allowed : 15.82 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1885 helix: 1.62 (0.18), residues: 861 sheet: 0.05 (0.42), residues: 156 loop : -0.97 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 63 TYR 0.022 0.001 TYR F 248 PHE 0.014 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.015 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00214 (15173) covalent geometry : angle 0.48426 (20570) hydrogen bonds : bond 0.03854 ( 713) hydrogen bonds : angle 4.60696 ( 2076) metal coordination : bond 0.00481 ( 5) metal coordination : angle 4.25406 ( 7) Misc. bond : bond 0.00032 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.549 Fit side-chains REVERT: A 343 ASN cc_start: 0.8337 (m-40) cc_final: 0.7941 (p0) REVERT: B 251 ASN cc_start: 0.8384 (t0) cc_final: 0.7987 (t0) REVERT: D 50 PHE cc_start: 0.7467 (t80) cc_final: 0.6585 (m-10) REVERT: F 108 ARG cc_start: 0.6759 (mtm-85) cc_final: 0.6123 (mtp180) REVERT: F 285 MET cc_start: 0.8542 (tpp) cc_final: 0.8254 (tpp) REVERT: F 346 ASP cc_start: 0.7071 (m-30) cc_final: 0.6698 (m-30) REVERT: F 360 TYR cc_start: 0.8339 (t80) cc_final: 0.7996 (t80) outliers start: 23 outliers final: 20 residues processed: 207 average time/residue: 0.1058 time to fit residues: 34.0103 Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 10.0000 chunk 149 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.139452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102202 restraints weight = 24735.762| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.86 r_work: 0.2852 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15180 Z= 0.175 Angle : 0.547 6.388 20577 Z= 0.282 Chirality : 0.043 0.172 2323 Planarity : 0.004 0.058 2573 Dihedral : 10.402 158.597 2310 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.43 % Allowed : 16.08 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1885 helix: 1.45 (0.18), residues: 858 sheet: 0.06 (0.42), residues: 154 loop : -0.94 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 260 TYR 0.029 0.001 TYR F 248 PHE 0.023 0.002 PHE F 24 TRP 0.024 0.002 TRP B 103 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00428 (15173) covalent geometry : angle 0.54328 (20570) hydrogen bonds : bond 0.04734 ( 713) hydrogen bonds : angle 4.70732 ( 2076) metal coordination : bond 0.00693 ( 5) metal coordination : angle 3.39593 ( 7) Misc. bond : bond 0.00075 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4147.54 seconds wall clock time: 71 minutes 20.38 seconds (4280.38 seconds total)