Starting phenix.real_space_refine on Tue Dec 31 12:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk4_33243/12_2024/7xk4_33243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk4_33243/12_2024/7xk4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk4_33243/12_2024/7xk4_33243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk4_33243/12_2024/7xk4_33243.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk4_33243/12_2024/7xk4_33243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk4_33243/12_2024/7xk4_33243.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 10.77, per 1000 atoms: 0.73 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: 4.73 Conformation dependent library (CDL) restraints added in 2.3 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: 1.57 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: 4.40 Time building geometry restraints manager: 4.64 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: 8803 35.47 - 70.93: 208 70.93 - 106.40: 9 106.40 - 141.87: 10 141.87 - 177.34: 4 Dihedral angle restraints: 9034 sinusoidal: 3668 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 9031 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 40.730 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.162 15173 Z= 0.471 Angle : 0.993 17.846 20570 Z= 0.599 Chirality : 0.054 0.473 2323 Planarity : 0.005 0.060 2571 Dihedral : 16.208 177.336 5612 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.030 0.002 PHE B 213 TYR 0.018 0.001 TYR F 217 ARG 0.005 0.000 ARG B 209 *********************** 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 : 1.652 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: 0.2734 time to fit residues: 99.2582 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 : 1.778 ------------------------------------------------------------------------------- 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 157 optimal weight: 20.0000 chunk 140 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 108 optimal weight: 0.3980 chunk 168 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 109 GLN A 215 HIS B 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15173 Z= 0.157 Angle : 0.523 8.818 20570 Z= 0.275 Chirality : 0.042 0.208 2323 Planarity : 0.004 0.059 2571 Dihedral : 13.738 177.033 2321 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.91 % Allowed : 8.50 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 1885 helix: 0.65 (0.18), residues: 847 sheet: -0.77 (0.38), residues: 160 loop : -1.58 (0.18), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS F 176 PHE 0.015 0.001 PHE D 104 TYR 0.016 0.001 TYR F 248 ARG 0.003 0.000 ARG A 330 *********************** 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 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.633 Fit side-chains REVERT: B 380 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: C 45 LYS cc_start: 0.7339 (ttpt) cc_final: 0.6682 (ttmt) REVERT: D 44 MET cc_start: 0.8964 (tpt) cc_final: 0.8593 (tpt) REVERT: D 65 HIS cc_start: 0.7942 (m170) cc_final: 0.7731 (m170) REVERT: E 51 ILE cc_start: 0.8545 (mt) cc_final: 0.8333 (mt) REVERT: F 346 ASP cc_start: 0.7124 (m-30) cc_final: 0.6836 (m-30) REVERT: F 360 TYR cc_start: 0.8132 (t80) cc_final: 0.7767 (t80) outliers start: 14 outliers final: 7 residues processed: 209 average time/residue: 0.2677 time to fit residues: 84.0300 Evaluate side-chains 193 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 206 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 208 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 242 GLN B 74 ASN D 137 ASN E 16 ASN F 175 HIS F 330 ASN F 356 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.084 15173 Z= 0.701 Angle : 0.795 10.215 20570 Z= 0.407 Chirality : 0.054 0.314 2323 Planarity : 0.006 0.075 2571 Dihedral : 13.804 173.494 2310 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.64 % Rotamer: Outliers : 2.66 % Allowed : 11.09 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 1885 helix: 0.34 (0.18), residues: 856 sheet: -0.66 (0.39), residues: 160 loop : -1.58 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 103 HIS 0.006 0.002 HIS B 330 PHE 0.027 0.003 PHE F 318 TYR 0.022 0.003 TYR F 248 ARG 0.012 0.001 ARG A 260 *********************** 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 227 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.675 Fit side-chains REVERT: A 46 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7186 (mtm-85) REVERT: C 110 GLN cc_start: 0.8659 (mt0) cc_final: 0.8214 (mt0) REVERT: F 257 LYS cc_start: 0.7691 (tptt) cc_final: 0.7339 (tptt) outliers start: 41 outliers final: 27 residues processed: 210 average time/residue: 0.2649 time to fit residues: 84.5121 Evaluate side-chains 202 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 171 ASN 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 119 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 0.0870 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15173 Z= 0.157 Angle : 0.514 8.925 20570 Z= 0.269 Chirality : 0.041 0.192 2323 Planarity : 0.004 0.058 2571 Dihedral : 12.699 176.654 2310 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.75 % Allowed : 13.23 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1885 helix: 1.07 (0.18), residues: 860 sheet: -0.37 (0.40), residues: 160 loop : -1.35 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.003 0.001 HIS B 46 PHE 0.017 0.001 PHE D 50 TYR 0.022 0.001 TYR F 248 ARG 0.002 0.000 ARG A 330 *********************** 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 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.828 Fit side-chains REVERT: A 142 ILE cc_start: 0.8716 (pt) cc_final: 0.8412 (mm) REVERT: C 110 GLN cc_start: 0.8614 (mt0) cc_final: 0.8197 (mt0) REVERT: D 63 ARG cc_start: 0.7789 (ptt-90) cc_final: 0.7413 (ptt-90) REVERT: F 257 LYS cc_start: 0.7617 (tptt) cc_final: 0.7364 (tptt) REVERT: F 346 ASP cc_start: 0.7166 (m-30) cc_final: 0.6838 (m-30) outliers start: 27 outliers final: 12 residues processed: 206 average time/residue: 0.2558 time to fit residues: 80.8758 Evaluate side-chains 191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL 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 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 9.9990 chunk 102 optimal weight: 0.0060 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 124 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 15173 Z= 0.160 Angle : 0.491 7.320 20570 Z= 0.256 Chirality : 0.041 0.153 2323 Planarity : 0.004 0.059 2571 Dihedral : 12.171 174.727 2310 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.49 % Allowed : 14.53 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1885 helix: 1.50 (0.18), residues: 848 sheet: -0.33 (0.39), residues: 167 loop : -1.17 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.005 0.001 HIS D 65 PHE 0.023 0.001 PHE F 24 TYR 0.023 0.001 TYR F 248 ARG 0.003 0.000 ARG F 303 *********************** 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 213 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 1.725 Fit side-chains REVERT: A 142 ILE cc_start: 0.8701 (pt) cc_final: 0.8465 (mm) REVERT: C 110 GLN cc_start: 0.8599 (mt0) cc_final: 0.8198 (mt0) REVERT: D 63 ARG cc_start: 0.7736 (ptt-90) cc_final: 0.7334 (ptt-90) REVERT: F 108 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.6489 (mtp180) REVERT: F 131 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6952 (pttt) REVERT: F 257 LYS cc_start: 0.7645 (tptt) cc_final: 0.7364 (tptt) REVERT: F 346 ASP cc_start: 0.7158 (m-30) cc_final: 0.6816 (m-30) outliers start: 23 outliers final: 17 residues processed: 204 average time/residue: 0.2657 time to fit residues: 81.8819 Evaluate side-chains 199 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 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 153 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 65 HIS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 131 LYS 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 60 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS E 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15173 Z= 0.430 Angle : 0.623 8.191 20570 Z= 0.321 Chirality : 0.047 0.225 2323 Planarity : 0.005 0.060 2571 Dihedral : 12.528 179.878 2310 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.40 % Allowed : 14.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 1885 helix: 1.08 (0.18), residues: 859 sheet: -0.21 (0.41), residues: 158 loop : -1.16 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 103 HIS 0.008 0.001 HIS D 65 PHE 0.024 0.002 PHE B 213 TYR 0.026 0.002 TYR F 248 ARG 0.009 0.001 ARG A 260 *********************** 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 229 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 1.696 Fit side-chains REVERT: A 46 ARG cc_start: 0.7559 (ttm110) cc_final: 0.7124 (mtm-85) REVERT: A 142 ILE cc_start: 0.8810 (pt) cc_final: 0.8442 (mm) REVERT: C 110 GLN cc_start: 0.8631 (mt0) cc_final: 0.8209 (mt0) REVERT: D 63 ARG cc_start: 0.7823 (ptt-90) cc_final: 0.7392 (ptt-90) REVERT: F 108 ARG cc_start: 0.6819 (mtm-85) cc_final: 0.6458 (mtp180) REVERT: F 257 LYS cc_start: 0.7599 (tptt) cc_final: 0.7389 (tptt) outliers start: 37 outliers final: 30 residues processed: 214 average time/residue: 0.2554 time to fit residues: 82.3089 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 : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL 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 D residue 171 ASN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 57 THR 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 240 VAL 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 173 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 131 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15173 Z= 0.188 Angle : 0.512 7.015 20570 Z= 0.266 Chirality : 0.042 0.159 2323 Planarity : 0.004 0.058 2571 Dihedral : 12.047 176.270 2308 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.75 % Allowed : 15.11 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1885 helix: 1.37 (0.18), residues: 861 sheet: -0.32 (0.40), residues: 165 loop : -1.07 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.008 0.001 HIS D 65 PHE 0.016 0.001 PHE B 213 TYR 0.024 0.001 TYR F 248 ARG 0.002 0.000 ARG A 260 *********************** 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 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.851 Fit side-chains REVERT: A 46 ARG cc_start: 0.7519 (ttm110) cc_final: 0.7113 (mtm-85) REVERT: A 142 ILE cc_start: 0.8742 (pt) cc_final: 0.8446 (mm) REVERT: C 49 ILE cc_start: 0.8606 (mt) cc_final: 0.8396 (mp) REVERT: C 110 GLN cc_start: 0.8606 (mt0) cc_final: 0.8203 (mt0) REVERT: D 50 PHE cc_start: 0.7309 (t80) cc_final: 0.6798 (m-10) REVERT: F 108 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.6488 (mtp180) outliers start: 27 outliers final: 20 residues processed: 204 average time/residue: 0.2661 time to fit residues: 82.5909 Evaluate side-chains 203 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 140 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15173 Z= 0.327 Angle : 0.578 10.795 20570 Z= 0.298 Chirality : 0.045 0.203 2323 Planarity : 0.004 0.058 2571 Dihedral : 12.107 178.439 2308 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.27 % Allowed : 14.85 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 1885 helix: 1.24 (0.18), residues: 860 sheet: -0.28 (0.41), residues: 153 loop : -1.06 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 103 HIS 0.005 0.001 HIS D 65 PHE 0.021 0.002 PHE B 213 TYR 0.024 0.002 TYR F 248 ARG 0.006 0.000 ARG A 260 *********************** 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 221 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 1.755 Fit side-chains REVERT: A 46 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7103 (mtm-85) REVERT: A 142 ILE cc_start: 0.8796 (pt) cc_final: 0.8444 (mm) REVERT: C 49 ILE cc_start: 0.8599 (mt) cc_final: 0.8367 (mp) REVERT: C 110 GLN cc_start: 0.8626 (mt0) cc_final: 0.8218 (mt0) REVERT: F 108 ARG cc_start: 0.6797 (mtm-85) cc_final: 0.6500 (mtp180) outliers start: 35 outliers final: 28 residues processed: 207 average time/residue: 0.2674 time to fit residues: 84.0456 Evaluate side-chains 212 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 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 171 ASN 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 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 0.0670 chunk 166 optimal weight: 5.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15173 Z= 0.304 Angle : 0.567 10.294 20570 Z= 0.293 Chirality : 0.044 0.199 2323 Planarity : 0.004 0.058 2571 Dihedral : 12.036 178.305 2308 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.27 % Allowed : 15.18 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 1885 helix: 1.24 (0.18), residues: 860 sheet: -0.25 (0.41), residues: 153 loop : -1.05 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 103 HIS 0.009 0.001 HIS D 65 PHE 0.020 0.002 PHE B 213 TYR 0.023 0.001 TYR F 248 ARG 0.005 0.000 ARG A 260 *********************** 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 222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.766 Fit side-chains REVERT: A 46 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7101 (mtm-85) REVERT: A 142 ILE cc_start: 0.8800 (pt) cc_final: 0.8443 (mm) REVERT: C 110 GLN cc_start: 0.8623 (mt0) cc_final: 0.8215 (mt0) REVERT: F 108 ARG cc_start: 0.6802 (mtm-85) cc_final: 0.6494 (mtp180) outliers start: 35 outliers final: 30 residues processed: 208 average time/residue: 0.2608 time to fit residues: 82.6058 Evaluate side-chains 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 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 D residue 171 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 57 THR 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 109 optimal weight: 0.6980 chunk 176 optimal weight: 0.4980 chunk 107 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 15173 Z= 0.160 Angle : 0.498 6.563 20570 Z= 0.260 Chirality : 0.041 0.162 2323 Planarity : 0.004 0.059 2571 Dihedral : 11.557 174.274 2308 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.62 % Allowed : 15.76 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1885 helix: 1.49 (0.18), residues: 867 sheet: -0.21 (0.41), residues: 156 loop : -0.91 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.026 0.001 HIS D 65 PHE 0.015 0.001 PHE B 213 TYR 0.021 0.001 TYR F 248 ARG 0.009 0.000 ARG D 63 ********************** 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 217 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 1.745 Fit side-chains REVERT: A 142 ILE cc_start: 0.8715 (pt) cc_final: 0.8459 (mm) REVERT: C 110 GLN cc_start: 0.8565 (mt0) cc_final: 0.8307 (mt0) REVERT: D 50 PHE cc_start: 0.7300 (t80) cc_final: 0.6802 (m-10) REVERT: F 108 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6456 (mtp180) outliers start: 25 outliers final: 22 residues processed: 209 average time/residue: 0.2508 time to fit residues: 81.1887 Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain 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 166 LEU Chi-restraints excluded: chain E residue 19 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 117 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 45 optimal weight: 0.0020 chunk 136 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.142785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.103501 restraints weight = 25970.027| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.87 r_work: 0.2905 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15173 Z= 0.173 Angle : 0.503 7.572 20570 Z= 0.261 Chirality : 0.042 0.201 2323 Planarity : 0.004 0.059 2571 Dihedral : 11.439 175.082 2308 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.82 % Allowed : 15.63 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1885 helix: 1.58 (0.18), residues: 862 sheet: -0.10 (0.41), residues: 156 loop : -0.89 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.009 0.001 HIS D 65 PHE 0.017 0.001 PHE B 213 TYR 0.022 0.001 TYR F 248 ARG 0.005 0.000 ARG D 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.65 seconds wall clock time: 59 minutes 29.60 seconds (3569.60 seconds total)