Starting phenix.real_space_refine on Fri Jul 3 18:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xk4_33243/07_2026/7xk4_33243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk4_33243/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xk4_33243/07_2026/7xk4_33243.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xk4_33243/07_2026/7xk4_33243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xk4_33243/07_2026/7xk4_33243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk4_33243/07_2026/7xk4_33243.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk4_33243/07_2026/7xk4_33243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk4_33243/07_2026/7xk4_33243.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.098 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14834 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 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 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 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: 3.50, per 1000 atoms: 0.24 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: 1.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.61 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: 1.97 Time building geometry restraints manager: 1.97 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: 20253 3.57 - 7.14: 272 7.14 - 10.71: 31 10.71 - 14.28: 12 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 - 35.47: 8660 35.47 - 70.93: 182 70.93 - 106.40: 8 106.40 - 141.87: 2 141.87 - 177.34: 4 Dihedral angle restraints: 8856 sinusoidal: 3490 harmonic: 5366 Sorted by residual: dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual -102.41 74.93 -177.34 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN C 301 " pdb=" C1' FMN C 301 " pdb=" N10 FMN C 301 " pdb=" C2' FMN C 301 " ideal model delta sinusoidal sigma weight residual -102.41 60.89 -163.30 1 2.00e+01 2.50e-03 4.70e+01 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 ... (remaining 8853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2171 0.095 - 0.189: 127 0.189 - 0.284: 17 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: 2571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.057 2.00e-02 2.50e+03 2.34e-02 2.61e+01 pdb=" C10 FMN C 301 " 0.007 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.024 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.013 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.013 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.032 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.011 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 " -0.005 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.055 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.026 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=" C1' FMN B 501 " -0.017 2.00e-02 2.50e+03 1.55e-02 1.15e+01 pdb=" C10 FMN B 501 " -0.005 2.00e-02 2.50e+03 pdb=" C2 FMN B 501 " 0.009 2.00e-02 2.50e+03 pdb=" C4 FMN B 501 " 0.003 2.00e-02 2.50e+03 pdb=" C4A FMN B 501 " -0.001 2.00e-02 2.50e+03 pdb=" C5A FMN B 501 " -0.020 2.00e-02 2.50e+03 pdb=" C6 FMN B 501 " -0.016 2.00e-02 2.50e+03 pdb=" C7 FMN B 501 " 0.009 2.00e-02 2.50e+03 pdb=" C7M FMN B 501 " 0.015 2.00e-02 2.50e+03 pdb=" C8 FMN B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C8M FMN B 501 " 0.031 2.00e-02 2.50e+03 pdb=" C9 FMN B 501 " -0.011 2.00e-02 2.50e+03 pdb=" C9A FMN B 501 " -0.012 2.00e-02 2.50e+03 pdb=" N1 FMN B 501 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FMN B 501 " -0.019 2.00e-02 2.50e+03 pdb=" N3 FMN B 501 " 0.002 2.00e-02 2.50e+03 pdb=" N5 FMN B 501 " -0.023 2.00e-02 2.50e+03 pdb=" O2 FMN B 501 " 0.028 2.00e-02 2.50e+03 pdb=" O4 FMN B 501 " 0.011 2.00e-02 2.50e+03 ... (remaining 2568 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 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= 0.551 Angle : 1.060 35.914 20577 Z= 0.601 Chirality : 0.054 0.473 2323 Planarity : 0.005 0.060 2571 Dihedral : 15.294 177.336 5434 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/Z covalent geometry : bond 0.00730 / 0.44 (15173) covalent geometry : angle 0.99345 / 0.60 (20570) hydrogen bonds : bond 0.16415 / 11.12 ( 713) hydrogen bonds : angle 6.91877 / 4.92 ( 2076) metal coordination : bond 0.77997 / 51.16 ( 5) metal coordination : angle 20.05003 / 9.74 ( 7) Misc. bond : bond 0.04388 / 2.19 ( 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 : 0.948 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: 0.1111 time to fit residues: 41.4857 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 : 0.592 ------------------------------------------------------------------------------- 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... 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 = 0.3529 r_free = 0.3529 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106109 restraints weight = 31951.561| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.62 r_work: 0.2816 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 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 = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1007 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= 0.155 Angle : 0.563 11.132 20577 Z= 0.293 Chirality : 0.043 0.212 2323 Planarity : 0.005 0.062 2571 Dihedral : 12.134 179.984 2143 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.23 % Allowed : 8.63 % Favored : 90.14 % 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: -0.88 (0.18), residues: 1885 helix: 0.49 (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 0.018 0.001 PHE D 50 TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (15173) covalent geometry : angle 0.55295 / 0.29 (20570) hydrogen bonds : bond 0.05014 / 3.45 ( 713) hydrogen bonds : angle 5.17949 / 3.60 ( 2076) metal coordination : bond 0.02143 / 1.54 ( 5) metal coordination : angle 5.80336 / 2.72 ( 7) Misc. bond : bond 0.00098 / 0.05 ( 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 : 0.504 Fit side-chains REVERT: A 172 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7415 (mp0) REVERT: D 44 MET cc_start: 0.8916 (tpt) cc_final: 0.8524 (tpt) REVERT: D 117 ARG cc_start: 0.8603 (mmp-170) cc_final: 0.8399 (mmp-170) REVERT: F 360 TYR cc_start: 0.8348 (t80) cc_final: 0.7838 (t80) outliers start: 19 outliers final: 11 residues processed: 203 average time/residue: 0.1013 time to fit residues: 31.3260 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 : 0.417 ------------------------------------------------------------------------------- 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: 0.7980 chunk 44 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN D 65 HIS D 137 ASN E 16 ASN F 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.141192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.104341 restraints weight = 31015.290| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.48 r_work: 0.2832 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1224 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= 0.174 Angle : 0.559 10.287 20577 Z= 0.290 Chirality : 0.043 0.184 2323 Planarity : 0.004 0.056 2571 Dihedral : 11.575 178.606 2134 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.62 % Allowed : 10.25 % Favored : 88.13 % 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: -0.34 (0.19), residues: 1885 helix: 1.00 (0.18), residues: 846 sheet: -0.50 (0.39), residues: 160 loop : -1.41 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.020 0.001 TYR F 248 PHE 0.021 0.002 PHE F 24 TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (15173) covalent geometry : angle 0.55506 / 0.29 (20570) hydrogen bonds : bond 0.05048 / 3.45 ( 713) hydrogen bonds : angle 4.95980 / 3.43 ( 2076) metal coordination : bond 0.00605 / 0.30 ( 5) metal coordination : angle 3.53284 / 1.53 ( 7) Misc. bond : bond 0.00121 / 0.06 ( 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 : 0.529 Fit side-chains REVERT: B 59 MET cc_start: 0.8739 (mmp) cc_final: 0.8232 (mmt) REVERT: C 49 ILE cc_start: 0.8396 (mt) cc_final: 0.8195 (mp) REVERT: D 44 MET cc_start: 0.8899 (tpt) cc_final: 0.8464 (tpt) REVERT: F 257 LYS cc_start: 0.7653 (tptt) cc_final: 0.7397 (tptt) outliers start: 25 outliers final: 15 residues processed: 204 average time/residue: 0.1146 time to fit residues: 36.0252 Evaluate side-chains 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 95 LEU 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: 0.8980 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 180 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 114 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107156 restraints weight = 33022.316| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.07 r_work: 0.2801 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15180 Z= 0.107 Angle : 0.489 8.943 20577 Z= 0.255 Chirality : 0.041 0.150 2323 Planarity : 0.004 0.058 2571 Dihedral : 11.072 174.719 2132 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.62 % Allowed : 11.87 % Favored : 86.51 % 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: 0.08 (0.19), residues: 1885 helix: 1.37 (0.18), residues: 854 sheet: -0.35 (0.39), residues: 170 loop : -1.23 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 303 TYR 0.021 0.001 TYR F 248 PHE 0.015 0.001 PHE D 50 TRP 0.022 0.001 TRP B 103 HIS 0.016 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15173) covalent geometry : angle 0.48595 / 0.25 (20570) hydrogen bonds : bond 0.04084 / 2.81 ( 713) hydrogen bonds : angle 4.72364 / 3.27 ( 2076) metal coordination : bond 0.00378 / 0.20 ( 5) metal coordination : angle 2.94759 / 1.29 ( 7) Misc. bond : bond 0.00069 / 0.04 ( 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 218 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.596 Fit side-chains REVERT: A 124 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7617 (mm-30) REVERT: E 197 GLN cc_start: 0.8521 (mt0) cc_final: 0.8300 (mt0) REVERT: F 214 MET cc_start: 0.8005 (mtm) cc_final: 0.7792 (mtm) REVERT: F 257 LYS cc_start: 0.7686 (tptt) cc_final: 0.7474 (tptt) REVERT: F 346 ASP cc_start: 0.7019 (m-30) cc_final: 0.6668 (m-30) REVERT: F 360 TYR cc_start: 0.8329 (t80) cc_final: 0.7948 (t80) outliers start: 25 outliers final: 15 residues processed: 210 average time/residue: 0.1096 time to fit residues: 35.7862 Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 49 MET 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: 0.0060 chunk 4 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 171 optimal weight: 0.1980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN F 112 GLN F 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.143881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.106303 restraints weight = 27114.560| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.05 r_work: 0.2912 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 15180 Z= 0.096 Angle : 0.466 7.550 20577 Z= 0.242 Chirality : 0.040 0.152 2323 Planarity : 0.004 0.059 2571 Dihedral : 10.482 173.529 2130 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.56 % Allowed : 12.84 % Favored : 85.60 % 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: 0.43 (0.19), residues: 1885 helix: 1.66 (0.18), residues: 858 sheet: -0.27 (0.38), residues: 177 loop : -1.05 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 63 TYR 0.025 0.001 TYR F 248 PHE 0.023 0.001 PHE F 24 TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (15173) covalent geometry : angle 0.46375 / 0.24 (20570) hydrogen bonds : bond 0.03691 / 2.54 ( 713) hydrogen bonds : angle 4.53821 / 3.13 ( 2076) metal coordination : bond 0.00232 / 0.12 ( 5) metal coordination : angle 2.46768 / 1.03 ( 7) Misc. bond : bond 0.00051 / 0.03 ( 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 226 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.549 Fit side-chains REVERT: A 142 ILE cc_start: 0.8736 (pt) cc_final: 0.8527 (mm) REVERT: A 170 GLN cc_start: 0.7631 (mt0) cc_final: 0.7154 (mt0) REVERT: B 251 ASN cc_start: 0.8369 (t0) cc_final: 0.7960 (t0) REVERT: C 95 LYS cc_start: 0.8469 (mmtp) cc_final: 0.8008 (tptt) REVERT: D 50 PHE cc_start: 0.7375 (t80) cc_final: 0.6586 (m-10) REVERT: E 197 GLN cc_start: 0.8498 (mt0) cc_final: 0.8289 (mt0) REVERT: F 257 LYS cc_start: 0.7713 (tptt) cc_final: 0.7457 (tptt) REVERT: F 285 MET cc_start: 0.8516 (tpp) cc_final: 0.8289 (tpp) REVERT: F 346 ASP cc_start: 0.7041 (m-30) cc_final: 0.6683 (m-30) REVERT: F 360 TYR cc_start: 0.8341 (t80) cc_final: 0.8065 (t80) outliers start: 24 outliers final: 15 residues processed: 219 average time/residue: 0.1133 time to fit residues: 38.5333 Evaluate side-chains 201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 146 LEU 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 D residue 49 MET 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: 4.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.141377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.103842 restraints weight = 36966.819| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.58 r_work: 0.2763 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15180 Z= 0.145 Angle : 0.508 7.055 20577 Z= 0.264 Chirality : 0.042 0.202 2323 Planarity : 0.004 0.059 2571 Dihedral : 10.546 175.661 2130 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.82 % Allowed : 13.55 % Favored : 84.63 % 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: 0.42 (0.19), residues: 1885 helix: 1.58 (0.18), residues: 858 sheet: -0.18 (0.39), residues: 175 loop : -0.99 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.026 0.001 TYR F 248 PHE 0.019 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/Z covalent geometry : bond 0.00350 / 0.14 (15173) covalent geometry : angle 0.50587 / 0.26 (20570) hydrogen bonds : bond 0.04350 / 2.99 ( 713) hydrogen bonds : angle 4.62303 / 3.18 ( 2076) metal coordination : bond 0.00544 / 0.28 ( 5) metal coordination : angle 2.62035 / 1.03 ( 7) Misc. bond : bond 0.00083 / 0.04 ( 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 214 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.610 Fit side-chains REVERT: A 142 ILE cc_start: 0.8792 (pt) cc_final: 0.8560 (mm) REVERT: A 170 GLN cc_start: 0.7671 (mt0) cc_final: 0.7189 (mt0) REVERT: B 251 ASN cc_start: 0.8394 (t0) cc_final: 0.8162 (t0) REVERT: C 95 LYS cc_start: 0.8472 (mmtp) cc_final: 0.8013 (tptt) REVERT: E 197 GLN cc_start: 0.8520 (mt0) cc_final: 0.8314 (mt0) REVERT: F 108 ARG cc_start: 0.6776 (mtm-85) cc_final: 0.6145 (mtp180) REVERT: F 115 VAL cc_start: 0.6765 (OUTLIER) cc_final: 0.6545 (t) REVERT: F 257 LYS cc_start: 0.7657 (tptt) cc_final: 0.7330 (tptt) REVERT: F 285 MET cc_start: 0.8547 (tpp) cc_final: 0.8307 (tpp) REVERT: F 346 ASP cc_start: 0.7072 (m-30) cc_final: 0.6694 (m-30) REVERT: F 360 TYR cc_start: 0.8306 (t80) cc_final: 0.7921 (t80) outliers start: 28 outliers final: 20 residues processed: 203 average time/residue: 0.1168 time to fit residues: 36.3180 Evaluate side-chains 201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 146 LEU 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 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain E residue 133 ASP 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: 0.5980 chunk 159 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 HIS F 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.138792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102094 restraints weight = 28994.067| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.31 r_work: 0.2803 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15180 Z= 0.247 Angle : 0.610 7.203 20577 Z= 0.314 Chirality : 0.046 0.226 2323 Planarity : 0.005 0.057 2571 Dihedral : 11.077 179.924 2130 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.46 % Allowed : 13.88 % Favored : 83.66 % 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: 0.14 (0.19), residues: 1885 helix: 1.20 (0.18), residues: 859 sheet: -0.17 (0.40), residues: 165 loop : -0.99 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 260 TYR 0.028 0.002 TYR F 248 PHE 0.022 0.002 PHE B 213 TRP 0.024 0.002 TRP B 103 HIS 0.005 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (15173) covalent geometry : angle 0.60598 / 0.31 (20570) hydrogen bonds : bond 0.05552 / 3.79 ( 713) hydrogen bonds : angle 4.89099 / 3.37 ( 2076) metal coordination : bond 0.01718 / 1.26 ( 5) metal coordination : angle 3.85854 / 1.84 ( 7) Misc. bond : bond 0.00153 / 0.08 ( 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 224 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.709 Fit side-chains REVERT: A 46 ARG cc_start: 0.7856 (ttm110) cc_final: 0.7305 (mtm-85) REVERT: A 142 ILE cc_start: 0.8830 (pt) cc_final: 0.8472 (mm) REVERT: A 170 GLN cc_start: 0.7804 (mt0) cc_final: 0.7598 (mt0) REVERT: B 59 MET cc_start: 0.8798 (mmp) cc_final: 0.8283 (mmt) REVERT: C 95 LYS cc_start: 0.8375 (mmtp) cc_final: 0.7888 (tptt) REVERT: E 197 GLN cc_start: 0.8518 (mt0) cc_final: 0.8280 (mt0) REVERT: F 108 ARG cc_start: 0.6671 (mtm-85) cc_final: 0.6033 (mtp180) REVERT: F 257 LYS cc_start: 0.7572 (tptt) cc_final: 0.7285 (tptt) REVERT: F 346 ASP cc_start: 0.7057 (m-30) cc_final: 0.6704 (m-30) REVERT: F 360 TYR cc_start: 0.8311 (t80) cc_final: 0.7808 (t80) outliers start: 38 outliers final: 31 residues processed: 208 average time/residue: 0.1176 time to fit residues: 37.3700 Evaluate side-chains 211 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 107 MET 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 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 E residue 19 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 57 THR 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: 0.9990 chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.139705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102641 restraints weight = 24706.147| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.85 r_work: 0.2852 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15180 Z= 0.147 Angle : 0.542 14.402 20577 Z= 0.277 Chirality : 0.043 0.179 2323 Planarity : 0.004 0.057 2571 Dihedral : 10.817 177.367 2130 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.95 % Allowed : 14.27 % Favored : 83.79 % 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: 0.29 (0.19), residues: 1885 helix: 1.38 (0.18), residues: 860 sheet: -0.15 (0.40), residues: 165 loop : -0.95 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.026 0.001 TYR F 248 PHE 0.018 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.006 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (15173) covalent geometry : angle 0.53056 / 0.28 (20570) hydrogen bonds : bond 0.04669 / 3.20 ( 713) hydrogen bonds : angle 4.76266 / 3.28 ( 2076) metal coordination : bond 0.01286 / 0.97 ( 5) metal coordination : angle 6.14769 / 3.39 ( 7) Misc. bond : bond 0.00089 / 0.04 ( 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 214 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.566 Fit side-chains REVERT: A 46 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7385 (mtm-85) REVERT: A 142 ILE cc_start: 0.8854 (pt) cc_final: 0.8569 (mm) REVERT: F 108 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6135 (mtp180) REVERT: F 257 LYS cc_start: 0.7658 (tptt) cc_final: 0.7431 (tptt) REVERT: F 346 ASP cc_start: 0.7087 (m-30) cc_final: 0.6687 (m-30) REVERT: F 360 TYR cc_start: 0.8327 (t80) cc_final: 0.7950 (t80) outliers start: 30 outliers final: 26 residues processed: 203 average time/residue: 0.1145 time to fit residues: 35.8826 Evaluate side-chains 207 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 107 MET 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 C residue 218 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain E residue 19 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 169 optimal weight: 0.1980 chunk 45 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105534 restraints weight = 36179.012| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.57 r_work: 0.2758 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15180 Z= 0.147 Angle : 0.528 8.270 20577 Z= 0.272 Chirality : 0.042 0.166 2323 Planarity : 0.004 0.057 2571 Dihedral : 10.657 176.408 2130 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.88 % Allowed : 14.79 % 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: 0.39 (0.19), residues: 1885 helix: 1.47 (0.18), residues: 861 sheet: -0.04 (0.42), residues: 154 loop : -0.92 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 63 TYR 0.025 0.001 TYR F 248 PHE 0.018 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (15173) covalent geometry : angle 0.52261 / 0.27 (20570) hydrogen bonds : bond 0.04540 / 3.12 ( 713) hydrogen bonds : angle 4.70957 / 3.25 ( 2076) metal coordination : bond 0.00720 / 0.46 ( 5) metal coordination : angle 4.13231 / 2.13 ( 7) Misc. bond : bond 0.00086 / 0.04 ( 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 208 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.556 Fit side-chains REVERT: A 46 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7245 (mtm-85) REVERT: A 142 ILE cc_start: 0.8815 (pt) cc_final: 0.8553 (mm) REVERT: D 50 PHE cc_start: 0.7392 (t80) cc_final: 0.6435 (m-10) REVERT: F 108 ARG cc_start: 0.6680 (mtm-85) cc_final: 0.6034 (mtp180) REVERT: F 346 ASP cc_start: 0.7024 (m-30) cc_final: 0.6608 (m-30) REVERT: F 360 TYR cc_start: 0.8301 (t80) cc_final: 0.7916 (t80) outliers start: 29 outliers final: 26 residues processed: 197 average time/residue: 0.1082 time to fit residues: 32.5839 Evaluate side-chains 203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 107 MET 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 16 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain E residue 19 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 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: 0.6980 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 115 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.105217 restraints weight = 28716.548| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.27 r_work: 0.2850 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15180 Z= 0.106 Angle : 0.493 7.767 20577 Z= 0.254 Chirality : 0.041 0.165 2323 Planarity : 0.004 0.058 2571 Dihedral : 10.393 174.448 2130 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.62 % Allowed : 15.11 % Favored : 83.27 % 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: 0.59 (0.19), residues: 1885 helix: 1.63 (0.18), residues: 864 sheet: 0.03 (0.42), residues: 156 loop : -0.82 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 303 TYR 0.023 0.001 TYR F 248 PHE 0.015 0.001 PHE B 213 TRP 0.021 0.001 TRP B 103 HIS 0.008 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15173) covalent geometry : angle 0.48719 / 0.25 (20570) hydrogen bonds : bond 0.03968 / 2.74 ( 713) hydrogen bonds : angle 4.59640 / 3.17 ( 2076) metal coordination : bond 0.00532 / 0.33 ( 5) metal coordination : angle 3.94265 / 2.04 ( 7) Misc. bond : bond 0.00053 / 0.03 ( 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 208 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.472 Fit side-chains REVERT: A 142 ILE cc_start: 0.8818 (pt) cc_final: 0.8612 (mm) REVERT: A 343 ASN cc_start: 0.8306 (m-40) cc_final: 0.7851 (p0) REVERT: D 50 PHE cc_start: 0.7401 (t80) cc_final: 0.6484 (m-10) REVERT: F 108 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6106 (mtp180) REVERT: F 257 LYS cc_start: 0.7594 (tptt) cc_final: 0.7215 (tptt) REVERT: F 285 MET cc_start: 0.8533 (tpp) cc_final: 0.8264 (tpp) REVERT: F 346 ASP cc_start: 0.7009 (m-30) cc_final: 0.6619 (m-30) REVERT: F 360 TYR cc_start: 0.8330 (t80) cc_final: 0.7970 (t80) outliers start: 25 outliers final: 23 residues processed: 199 average time/residue: 0.1095 time to fit residues: 33.4564 Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 107 MET Chi-restraints excluded: chain B residue 123 LEU 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 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 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 44 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 131 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103591 restraints weight = 24434.423| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.88 r_work: 0.2826 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15180 Z= 0.217 Angle : 0.581 6.539 20577 Z= 0.299 Chirality : 0.045 0.195 2323 Planarity : 0.004 0.057 2571 Dihedral : 10.735 178.464 2130 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.88 % Allowed : 14.92 % Favored : 83.20 % 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: 0.35 (0.19), residues: 1885 helix: 1.35 (0.18), residues: 864 sheet: 0.01 (0.42), residues: 154 loop : -0.86 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 260 TYR 0.025 0.002 TYR F 248 PHE 0.022 0.002 PHE B 213 TRP 0.024 0.002 TRP B 103 HIS 0.012 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 (15173) covalent geometry : angle 0.57756 / 0.30 (20570) hydrogen bonds : bond 0.05131 / 3.51 ( 713) hydrogen bonds : angle 4.76578 / 3.28 ( 2076) metal coordination : bond 0.00766 / 0.38 ( 5) metal coordination : angle 3.26156 / 1.48 ( 7) Misc. bond : bond 0.00132 / 0.07 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.83 seconds wall clock time: 71 minutes 58.29 seconds (4318.29 seconds total)