Starting phenix.real_space_refine on Tue Dec 31 15:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk6_33245/12_2024/7xk6_33245.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk6_33245/12_2024/7xk6_33245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk6_33245/12_2024/7xk6_33245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk6_33245/12_2024/7xk6_33245.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk6_33245/12_2024/7xk6_33245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk6_33245/12_2024/7xk6_33245.cif" } resolution = 3.0 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= 0.004 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9778 2.51 5 N 2448 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15123 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3173 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 396} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1558 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1507 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 221 Unusual residues: {'0NI': 1, 'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8663 SG CYS D 29 45.569 69.551 91.992 1.00 50.25 S ATOM 10264 SG CYS E 26 43.772 72.562 87.829 1.00 51.15 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 338 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 338 " occ=0.50 Time building chain proxies: 11.70, per 1000 atoms: 0.77 Number of scatterers: 15123 At special positions: 0 Unit cell: (91.52, 126.72, 155.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2794 8.00 N 2448 7.00 C 9778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 111 " Number of angles added : 7 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3466 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 12 sheets defined 52.1% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.934A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.629A pdb=" N THR A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 410 through 413 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.931A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.526A pdb=" N ILE B 10 " --> pdb=" O PHE B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.952A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.756A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.784A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.513A pdb=" N LEU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.703A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.711A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.559A pdb=" N LYS B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.559A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 236 through 239 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 246 through 249 removed outlier: 3.562A pdb=" N LEU B 249 " --> pdb=" O ALA B 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.665A pdb=" N ALA B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.632A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.511A pdb=" N PHE B 323 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 324' Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.048A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 353 through 374 removed outlier: 4.031A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.949A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.593A pdb=" N ASP B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.530A pdb=" N VAL C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 4.163A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.149A pdb=" N GLN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.656A pdb=" N ASN C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.835A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 8 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 35 removed outlier: 3.788A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.522A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.534A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.686A pdb=" N ILE D 108 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.045A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.719A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 removed outlier: 3.762A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 184 through 202 removed outlier: 4.539A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 removed outlier: 3.623A pdb=" N VAL D 206 " --> pdb=" O PRO D 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 206' Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.679A pdb=" N LEU E 7 " --> pdb=" O HIS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 removed outlier: 3.927A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.961A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 98 removed outlier: 3.567A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 124 through 128 Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 185 through 188 Processing helix chain 'F' and resid 189 through 196 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 244 through 252 removed outlier: 3.516A pdb=" N TRP F 250 " --> pdb=" O SER F 246 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 252 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.915A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 328 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 369 through 373 removed outlier: 3.623A pdb=" N CYS F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 393 removed outlier: 3.573A pdb=" N ALA F 385 " --> pdb=" O PRO F 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.393A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.543A pdb=" N LEU A 274 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 307 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.567A pdb=" N ASN A 80 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL A 90 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU A 78 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE A 92 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 76 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 74 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.181A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 4.022A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 15.057A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.505A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR C 150 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 154 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 164 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU C 156 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL C 162 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'F' and resid 37 through 38 removed outlier: 6.062A pdb=" N SER F 38 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU F 122 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE F 83 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 208 through 213 removed outlier: 3.506A pdb=" N ILE F 208 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 260 " --> pdb=" O TRP F 133 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB3, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.391A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 339 " --> pdb=" O TYR F 351 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 701 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 4890 1.37 - 1.58: 10363 1.58 - 1.78: 14 1.78 - 1.99: 148 1.99 - 2.20: 8 Bond restraints: 15423 Sorted by residual: bond pdb=" C4A RBF B 601 " pdb=" N5 RBF B 601 " ideal model delta sigma weight residual 1.288 1.447 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" C10 RBF B 601 " pdb=" N1 RBF B 601 " ideal model delta sigma weight residual 1.304 1.460 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" C5A RBF B 601 " pdb=" N5 RBF B 601 " ideal model delta sigma weight residual 1.350 1.488 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.528 1.436 0.092 1.34e-02 5.57e+03 4.73e+01 bond pdb=" C PRO B 217 " pdb=" O PRO B 217 " ideal model delta sigma weight residual 1.235 1.163 0.071 1.11e-02 8.12e+03 4.11e+01 ... (remaining 15418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 20532 3.36 - 6.71: 315 6.71 - 10.07: 39 10.07 - 13.43: 12 13.43 - 16.79: 4 Bond angle restraints: 20902 Sorted by residual: angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.64 13.69 1.14e+00 7.69e-01 1.44e+02 angle pdb=" S1 FES F 501 " pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.63 13.70 1.20e+00 6.94e-01 1.30e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 88.59 -12.93 1.14e+00 7.69e-01 1.29e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 91.46 12.87 1.14e+00 7.69e-01 1.27e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 88.37 -12.71 1.14e+00 7.69e-01 1.24e+02 ... (remaining 20897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8937 35.47 - 70.94: 219 70.94 - 106.41: 16 106.41 - 141.87: 8 141.87 - 177.34: 7 Dihedral angle restraints: 9187 sinusoidal: 3752 harmonic: 5435 Sorted by residual: dihedral pdb=" CA HIS A 215 " pdb=" C HIS A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 121.90 58.10 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SER F 99 " pdb=" C SER F 99 " pdb=" N LYS F 100 " pdb=" CA LYS F 100 " ideal model delta harmonic sigma weight residual 180.00 -127.22 -52.78 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA GLN D 24 " pdb=" C GLN D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta harmonic sigma weight residual -180.00 -142.93 -37.07 0 5.00e+00 4.00e-02 5.50e+01 ... (remaining 9184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2217 0.104 - 0.208: 111 0.208 - 0.312: 14 0.312 - 0.415: 3 0.415 - 0.519: 4 Chirality restraints: 2349 Sorted by residual: chirality pdb=" CA PRO C 174 " pdb=" N PRO C 174 " pdb=" C PRO C 174 " pdb=" CB PRO C 174 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA PRO B 379 " pdb=" N PRO B 379 " pdb=" C PRO B 379 " pdb=" CB PRO B 379 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.92e+00 ... (remaining 2346 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 0NI B 602 " 0.280 2.00e-02 2.50e+03 2.36e-01 6.98e+02 pdb=" C16 0NI B 602 " -0.398 2.00e-02 2.50e+03 pdb=" C17 0NI B 602 " -0.089 2.00e-02 2.50e+03 pdb=" C18 0NI B 602 " 0.022 2.00e-02 2.50e+03 pdb=" C19 0NI B 602 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0NI B 602 " -0.073 2.00e-02 2.50e+03 6.13e-02 4.70e+01 pdb=" C11 0NI B 602 " 0.097 2.00e-02 2.50e+03 pdb=" C12 0NI B 602 " 0.025 2.00e-02 2.50e+03 pdb=" C13 0NI B 602 " 0.010 2.00e-02 2.50e+03 pdb=" C14 0NI B 602 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " -0.069 2.00e-02 2.50e+03 2.83e-02 3.82e+01 pdb=" C10 FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " 0.027 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " -0.016 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " 0.033 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " 0.026 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " 0.025 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " 0.067 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " -0.017 2.00e-02 2.50e+03 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 270 2.68 - 3.24: 14042 3.24 - 3.79: 22083 3.79 - 4.35: 32122 4.35 - 4.90: 53627 Nonbonded interactions: 122144 Sorted by model distance: nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.129 3.040 nonbonded pdb=" NH1 ARG F 80 " pdb=" OE1 GLU F 107 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR B 87 " pdb=" O ASP B 230 " model vdw 2.207 3.040 nonbonded pdb=" O LEU F 95 " pdb=" OG SER F 99 " model vdw 2.221 3.040 nonbonded pdb=" O4' FMN B 600 " pdb=" O5' FMN B 600 " model vdw 2.225 2.432 ... (remaining 122139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 43.020 Find NCS groups from input model: 0.260 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:13.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.159 15423 Z= 0.475 Angle : 1.014 16.787 20902 Z= 0.607 Chirality : 0.057 0.519 2349 Planarity : 0.008 0.236 2612 Dihedral : 16.488 177.342 5721 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.36 % Favored : 96.33 % Rotamer: Outliers : 0.70 % Allowed : 2.94 % Favored : 96.35 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.16 % Rama-Z (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: -2.57 (0.16), residues: 1910 helix: -1.08 (0.16), residues: 835 sheet: -1.38 (0.37), residues: 168 loop : -2.36 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 146 HIS 0.004 0.001 HIS A 215 PHE 0.034 0.002 PHE B 213 TYR 0.041 0.002 TYR B 412 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.764 Fit side-chains REVERT: A 75 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7158 (tttt) REVERT: A 396 ASP cc_start: 0.8098 (m-30) cc_final: 0.7774 (m-30) REVERT: A 404 SER cc_start: 0.8884 (t) cc_final: 0.8581 (m) REVERT: B 9 ASP cc_start: 0.7221 (m-30) cc_final: 0.7003 (m-30) REVERT: B 151 ARG cc_start: 0.7889 (mmm160) cc_final: 0.6415 (mpt180) REVERT: C 110 GLN cc_start: 0.8493 (mt0) cc_final: 0.8035 (mt0) REVERT: C 116 GLN cc_start: 0.7774 (mt0) cc_final: 0.7556 (mt0) REVERT: C 129 ASP cc_start: 0.7253 (t0) cc_final: 0.6302 (p0) REVERT: D 68 ASN cc_start: 0.7504 (m110) cc_final: 0.6989 (t0) REVERT: D 96 ASP cc_start: 0.7205 (m-30) cc_final: 0.6949 (m-30) REVERT: D 210 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5798 (tp30) REVERT: E 10 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7836 (ttmm) REVERT: E 15 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7677 (pt0) REVERT: E 101 PHE cc_start: 0.7390 (m-80) cc_final: 0.7039 (m-80) REVERT: F 126 GLU cc_start: 0.6407 (mp0) cc_final: 0.6166 (mp0) REVERT: F 200 TYR cc_start: 0.6778 (m-80) cc_final: 0.6500 (m-80) REVERT: F 383 MET cc_start: 0.7800 (ttp) cc_final: 0.7591 (ttp) outliers start: 11 outliers final: 5 residues processed: 212 average time/residue: 1.4890 time to fit residues: 344.4233 Evaluate side-chains 146 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 174 PRO Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 171 optimal weight: 0.0370 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 88 GLN A 109 GLN A 215 HIS B 74 ASN B 78 GLN B 156 ASN B 178 GLN B 219 GLN B 243 GLN B 354 ASN B 404 ASN C 37 GLN C 46 GLN C 120 ASN C 160 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 88 GLN D 100 GLN D 205 GLN E 79 ASN E 107 ASN F 78 GLN F 140 ASN F 176 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15423 Z= 0.224 Angle : 0.577 8.660 20902 Z= 0.304 Chirality : 0.044 0.163 2349 Planarity : 0.005 0.116 2612 Dihedral : 14.309 178.673 2371 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.66 % Allowed : 9.60 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.11 % 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: -1.12 (0.18), residues: 1910 helix: 0.29 (0.18), residues: 853 sheet: -0.78 (0.39), residues: 160 loop : -1.76 (0.18), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS B 46 PHE 0.017 0.001 PHE C 235 TYR 0.015 0.001 TYR D 141 ARG 0.005 0.000 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.840 Fit side-chains REVERT: A 75 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7120 (tttt) REVERT: A 396 ASP cc_start: 0.7964 (m-30) cc_final: 0.7668 (m-30) REVERT: A 404 SER cc_start: 0.8813 (t) cc_final: 0.8462 (m) REVERT: B 107 MET cc_start: 0.8501 (ttm) cc_final: 0.8170 (ttm) REVERT: B 151 ARG cc_start: 0.7942 (mmm160) cc_final: 0.6344 (mpt180) REVERT: C 110 GLN cc_start: 0.8566 (mt0) cc_final: 0.8269 (mt0) REVERT: C 116 GLN cc_start: 0.7731 (mt0) cc_final: 0.7476 (mt0) REVERT: C 129 ASP cc_start: 0.7183 (t0) cc_final: 0.6365 (p0) REVERT: C 242 MET cc_start: 0.8347 (mmm) cc_final: 0.8116 (tpp) REVERT: D 68 ASN cc_start: 0.7243 (m110) cc_final: 0.6667 (t0) REVERT: D 210 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5788 (tp30) REVERT: E 101 PHE cc_start: 0.7222 (m-80) cc_final: 0.6890 (m-80) REVERT: E 102 PHE cc_start: 0.6244 (m-80) cc_final: 0.5981 (m-80) REVERT: F 126 GLU cc_start: 0.6479 (mp0) cc_final: 0.6264 (mp0) REVERT: F 200 TYR cc_start: 0.6960 (m-80) cc_final: 0.6698 (m-80) REVERT: F 382 MET cc_start: 0.6873 (ttm) cc_final: 0.6624 (mtp) outliers start: 26 outliers final: 8 residues processed: 170 average time/residue: 1.5110 time to fit residues: 281.4594 Evaluate side-chains 146 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 0.0370 chunk 47 optimal weight: 7.9990 chunk 171 optimal weight: 0.0060 chunk 185 optimal weight: 5.9990 chunk 153 optimal weight: 0.0970 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.5674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15423 Z= 0.138 Angle : 0.491 8.134 20902 Z= 0.259 Chirality : 0.041 0.157 2349 Planarity : 0.005 0.103 2612 Dihedral : 12.249 179.517 2363 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.11 % Allowed : 10.05 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % 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: -0.24 (0.19), residues: 1910 helix: 1.10 (0.18), residues: 852 sheet: -0.59 (0.39), residues: 178 loop : -1.35 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS A 215 PHE 0.014 0.001 PHE B 213 TYR 0.011 0.001 TYR D 141 ARG 0.006 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.816 Fit side-chains REVERT: A 75 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7098 (tttt) REVERT: A 396 ASP cc_start: 0.7904 (m-30) cc_final: 0.7675 (m-30) REVERT: A 404 SER cc_start: 0.8700 (t) cc_final: 0.8301 (m) REVERT: B 5 LYS cc_start: 0.7293 (tmmt) cc_final: 0.7046 (tttp) REVERT: B 107 MET cc_start: 0.8504 (ttm) cc_final: 0.8217 (ttm) REVERT: B 151 ARG cc_start: 0.7850 (mmm160) cc_final: 0.6255 (mpt180) REVERT: C 129 ASP cc_start: 0.7209 (t0) cc_final: 0.6393 (p0) REVERT: D 49 MET cc_start: 0.8235 (mtp) cc_final: 0.7875 (mtm) REVERT: D 63 ARG cc_start: 0.7738 (ptt-90) cc_final: 0.7100 (ttp-110) REVERT: D 68 ASN cc_start: 0.7121 (m110) cc_final: 0.6589 (t0) REVERT: D 119 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: D 210 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.5731 (tp30) REVERT: E 101 PHE cc_start: 0.7187 (m-80) cc_final: 0.6839 (m-80) REVERT: F 200 TYR cc_start: 0.6862 (m-80) cc_final: 0.6646 (m-80) REVERT: F 203 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.5626 (ptpt) outliers start: 33 outliers final: 9 residues processed: 177 average time/residue: 1.4132 time to fit residues: 276.0304 Evaluate side-chains 150 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 0.1980 chunk 182 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 251 ASN D 18 ASN D 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15423 Z= 0.316 Angle : 0.584 8.328 20902 Z= 0.305 Chirality : 0.045 0.166 2349 Planarity : 0.005 0.124 2612 Dihedral : 11.714 179.004 2360 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.98 % Allowed : 11.78 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % 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: -0.27 (0.19), residues: 1910 helix: 1.03 (0.18), residues: 861 sheet: -0.51 (0.40), residues: 162 loop : -1.33 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS B 330 PHE 0.022 0.002 PHE B 213 TYR 0.018 0.002 TYR D 141 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.703 Fit side-chains REVERT: A 75 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7142 (tttt) REVERT: A 171 SER cc_start: 0.7577 (OUTLIER) cc_final: 0.7268 (m) REVERT: A 396 ASP cc_start: 0.7980 (m-30) cc_final: 0.7679 (m-30) REVERT: A 404 SER cc_start: 0.8694 (t) cc_final: 0.8409 (m) REVERT: B 5 LYS cc_start: 0.7334 (tmmt) cc_final: 0.7056 (tttp) REVERT: B 107 MET cc_start: 0.8609 (ttm) cc_final: 0.8304 (ttm) REVERT: B 151 ARG cc_start: 0.8040 (mmm160) cc_final: 0.6411 (mpt180) REVERT: B 380 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: B 409 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 129 ASP cc_start: 0.7281 (t0) cc_final: 0.6555 (p0) REVERT: D 49 MET cc_start: 0.8235 (mtp) cc_final: 0.7878 (mtm) REVERT: D 68 ASN cc_start: 0.7282 (m110) cc_final: 0.6756 (t0) REVERT: D 119 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: D 210 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5728 (tp30) REVERT: E 101 PHE cc_start: 0.7199 (m-80) cc_final: 0.6824 (m-80) REVERT: F 119 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6927 (mmm) REVERT: F 200 TYR cc_start: 0.6951 (m-80) cc_final: 0.6680 (m-80) REVERT: F 244 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8246 (pt0) REVERT: F 382 MET cc_start: 0.6924 (ttm) cc_final: 0.6660 (mtp) outliers start: 31 outliers final: 15 residues processed: 158 average time/residue: 1.4316 time to fit residues: 248.6147 Evaluate side-chains 153 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15423 Z= 0.385 Angle : 0.636 8.350 20902 Z= 0.331 Chirality : 0.047 0.184 2349 Planarity : 0.005 0.118 2612 Dihedral : 11.650 179.951 2360 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.56 % Allowed : 12.74 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.16 % 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: 1910 helix: 0.88 (0.18), residues: 862 sheet: -0.60 (0.41), residues: 162 loop : -1.35 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 PHE 0.023 0.002 PHE B 213 TYR 0.019 0.002 TYR D 141 ARG 0.006 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.788 Fit side-chains REVERT: A 75 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7104 (tttt) REVERT: A 171 SER cc_start: 0.7551 (OUTLIER) cc_final: 0.7318 (m) REVERT: A 404 SER cc_start: 0.8744 (t) cc_final: 0.8469 (m) REVERT: B 5 LYS cc_start: 0.7319 (tmmt) cc_final: 0.7014 (tttp) REVERT: B 107 MET cc_start: 0.8594 (ttm) cc_final: 0.8279 (ttm) REVERT: B 151 ARG cc_start: 0.8058 (mmm160) cc_final: 0.6403 (mpt180) REVERT: B 380 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: C 129 ASP cc_start: 0.7353 (t0) cc_final: 0.6512 (p0) REVERT: D 49 MET cc_start: 0.8251 (mtp) cc_final: 0.7886 (mtm) REVERT: D 68 ASN cc_start: 0.7526 (m110) cc_final: 0.6970 (t0) REVERT: D 119 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: D 210 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5715 (tp30) REVERT: E 98 LEU cc_start: 0.6798 (mt) cc_final: 0.6593 (mt) REVERT: F 119 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6575 (mmt) REVERT: F 200 TYR cc_start: 0.6941 (m-80) cc_final: 0.6672 (m-80) REVERT: F 244 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8384 (pt0) REVERT: F 312 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7638 (mtp180) REVERT: F 317 MET cc_start: 0.7617 (mtp) cc_final: 0.7416 (mtp) REVERT: F 382 MET cc_start: 0.7037 (ttm) cc_final: 0.6760 (mtp) outliers start: 40 outliers final: 20 residues processed: 164 average time/residue: 1.5149 time to fit residues: 273.0290 Evaluate side-chains 155 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 70 CYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 312 ARG Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.4980 chunk 164 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 182 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN F 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15423 Z= 0.158 Angle : 0.496 7.709 20902 Z= 0.262 Chirality : 0.041 0.156 2349 Planarity : 0.005 0.106 2612 Dihedral : 10.781 179.712 2360 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.22 % Allowed : 14.79 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 1910 helix: 1.32 (0.18), residues: 861 sheet: -0.46 (0.39), residues: 178 loop : -1.10 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS A 215 PHE 0.014 0.001 PHE B 213 TYR 0.013 0.001 TYR D 141 ARG 0.008 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.850 Fit side-chains REVERT: A 75 LYS cc_start: 0.7674 (ttmm) cc_final: 0.7071 (tttt) REVERT: A 171 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7164 (m) REVERT: A 396 ASP cc_start: 0.7933 (m-30) cc_final: 0.7633 (m-30) REVERT: A 404 SER cc_start: 0.8545 (t) cc_final: 0.8340 (m) REVERT: B 5 LYS cc_start: 0.7385 (tmmt) cc_final: 0.7082 (tttp) REVERT: B 107 MET cc_start: 0.8536 (ttm) cc_final: 0.8258 (ttm) REVERT: B 151 ARG cc_start: 0.8044 (mmm160) cc_final: 0.6305 (mpt180) REVERT: C 129 ASP cc_start: 0.7298 (t0) cc_final: 0.6486 (p0) REVERT: D 68 ASN cc_start: 0.7314 (m110) cc_final: 0.6816 (t0) REVERT: F 119 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6622 (mmm) REVERT: F 200 TYR cc_start: 0.6870 (m-80) cc_final: 0.6646 (m-80) REVERT: F 244 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: F 382 MET cc_start: 0.6928 (ttm) cc_final: 0.6655 (mtp) outliers start: 19 outliers final: 11 residues processed: 156 average time/residue: 1.4535 time to fit residues: 249.8530 Evaluate side-chains 148 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.5980 chunk 20 optimal weight: 0.0370 chunk 104 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN F 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15423 Z= 0.147 Angle : 0.485 8.480 20902 Z= 0.255 Chirality : 0.041 0.157 2349 Planarity : 0.005 0.125 2612 Dihedral : 10.359 179.276 2360 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.41 % Allowed : 14.98 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % 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: 0.38 (0.19), residues: 1910 helix: 1.54 (0.18), residues: 858 sheet: -0.41 (0.39), residues: 178 loop : -0.92 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.005 0.001 HIS A 215 PHE 0.016 0.001 PHE B 213 TYR 0.014 0.001 TYR D 141 ARG 0.007 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.875 Fit side-chains REVERT: A 75 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7119 (pttt) REVERT: A 396 ASP cc_start: 0.7864 (m-30) cc_final: 0.7628 (m-30) REVERT: A 404 SER cc_start: 0.8546 (t) cc_final: 0.8233 (m) REVERT: B 5 LYS cc_start: 0.7390 (tmmt) cc_final: 0.7074 (tttp) REVERT: B 107 MET cc_start: 0.8531 (ttm) cc_final: 0.8306 (ttm) REVERT: B 151 ARG cc_start: 0.8031 (mmm160) cc_final: 0.6352 (mpt180) REVERT: C 129 ASP cc_start: 0.7294 (t0) cc_final: 0.6676 (p0) REVERT: D 68 ASN cc_start: 0.7370 (m110) cc_final: 0.6852 (t0) REVERT: D 119 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: F 119 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6609 (mmm) REVERT: F 200 TYR cc_start: 0.6867 (m-80) cc_final: 0.6640 (m-80) REVERT: F 382 MET cc_start: 0.6871 (ttm) cc_final: 0.6591 (mtp) outliers start: 22 outliers final: 14 residues processed: 150 average time/residue: 1.4043 time to fit residues: 232.0049 Evaluate side-chains 147 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 165 optimal weight: 0.0570 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN F 356 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15423 Z= 0.226 Angle : 0.529 8.480 20902 Z= 0.277 Chirality : 0.043 0.163 2349 Planarity : 0.005 0.125 2612 Dihedral : 10.483 178.658 2357 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.54 % Allowed : 14.79 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 0.27 (0.19), residues: 1910 helix: 1.43 (0.18), residues: 860 sheet: -0.47 (0.40), residues: 168 loop : -0.94 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.006 0.001 HIS B 153 PHE 0.019 0.001 PHE B 213 TYR 0.018 0.001 TYR D 141 ARG 0.007 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.856 Fit side-chains REVERT: A 75 LYS cc_start: 0.7739 (ttmm) cc_final: 0.7138 (tttt) REVERT: A 171 SER cc_start: 0.7453 (OUTLIER) cc_final: 0.7215 (m) REVERT: A 388 MET cc_start: 0.9029 (mtt) cc_final: 0.8797 (mtt) REVERT: A 396 ASP cc_start: 0.7964 (m-30) cc_final: 0.7748 (m-30) REVERT: A 404 SER cc_start: 0.8583 (t) cc_final: 0.8329 (m) REVERT: B 5 LYS cc_start: 0.7410 (tmmt) cc_final: 0.7077 (tttp) REVERT: B 107 MET cc_start: 0.8544 (ttm) cc_final: 0.8214 (ttm) REVERT: B 151 ARG cc_start: 0.8056 (mmm160) cc_final: 0.6423 (mpt180) REVERT: B 391 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8212 (mt) REVERT: D 49 MET cc_start: 0.8224 (mtp) cc_final: 0.7860 (mtm) REVERT: D 68 ASN cc_start: 0.7454 (m110) cc_final: 0.6959 (t0) REVERT: D 96 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7144 (p0) REVERT: D 119 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: F 119 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6618 (mmm) REVERT: F 200 TYR cc_start: 0.6868 (m-80) cc_final: 0.6631 (m-80) REVERT: F 244 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: F 382 MET cc_start: 0.6982 (ttm) cc_final: 0.6713 (mtp) outliers start: 24 outliers final: 14 residues processed: 150 average time/residue: 1.4970 time to fit residues: 247.0906 Evaluate side-chains 150 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15423 Z= 0.208 Angle : 0.519 7.689 20902 Z= 0.273 Chirality : 0.042 0.157 2349 Planarity : 0.005 0.121 2612 Dihedral : 10.427 178.693 2357 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.66 % Allowed : 15.11 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % 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: 0.30 (0.19), residues: 1910 helix: 1.44 (0.18), residues: 866 sheet: -0.47 (0.40), residues: 168 loop : -0.93 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.018 0.001 PHE B 213 TYR 0.016 0.001 TYR D 141 ARG 0.012 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.760 Fit side-chains REVERT: A 75 LYS cc_start: 0.7742 (ttmm) cc_final: 0.7142 (pttt) REVERT: A 171 SER cc_start: 0.7452 (OUTLIER) cc_final: 0.7214 (m) REVERT: A 388 MET cc_start: 0.9040 (mtt) cc_final: 0.8799 (mtt) REVERT: A 396 ASP cc_start: 0.7959 (m-30) cc_final: 0.7661 (m-30) REVERT: B 5 LYS cc_start: 0.7418 (tmmt) cc_final: 0.7086 (tttp) REVERT: B 107 MET cc_start: 0.8527 (ttm) cc_final: 0.8236 (ttm) REVERT: B 151 ARG cc_start: 0.8026 (mmm160) cc_final: 0.6445 (mpt180) REVERT: B 391 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8241 (mt) REVERT: D 49 MET cc_start: 0.8244 (mtp) cc_final: 0.7872 (mtm) REVERT: D 68 ASN cc_start: 0.7482 (m110) cc_final: 0.6979 (t0) REVERT: D 96 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7122 (p0) REVERT: D 119 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: F 119 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6610 (mmm) REVERT: F 200 TYR cc_start: 0.6920 (m-80) cc_final: 0.6684 (m-80) REVERT: F 244 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: F 382 MET cc_start: 0.7004 (ttm) cc_final: 0.6727 (mtp) outliers start: 26 outliers final: 16 residues processed: 150 average time/residue: 1.4231 time to fit residues: 234.4215 Evaluate side-chains 149 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15423 Z= 0.231 Angle : 0.532 7.689 20902 Z= 0.279 Chirality : 0.043 0.160 2349 Planarity : 0.005 0.122 2612 Dihedral : 10.456 178.659 2357 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.60 % Allowed : 15.11 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % 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: 0.25 (0.19), residues: 1910 helix: 1.39 (0.18), residues: 868 sheet: -0.49 (0.40), residues: 168 loop : -0.95 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.019 0.001 PHE B 213 TYR 0.018 0.001 TYR D 141 ARG 0.008 0.000 ARG D 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 1.736 Fit side-chains REVERT: A 75 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7123 (tttt) REVERT: A 171 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7239 (m) REVERT: A 388 MET cc_start: 0.9050 (mtt) cc_final: 0.8783 (mtt) REVERT: A 396 ASP cc_start: 0.7973 (m-30) cc_final: 0.7651 (m-30) REVERT: B 5 LYS cc_start: 0.7387 (tmmt) cc_final: 0.7048 (tttp) REVERT: B 107 MET cc_start: 0.8558 (ttm) cc_final: 0.8209 (ttm) REVERT: B 151 ARG cc_start: 0.8032 (mmm160) cc_final: 0.6436 (mpt180) REVERT: B 391 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8221 (mt) REVERT: D 49 MET cc_start: 0.8249 (mtp) cc_final: 0.7879 (mtm) REVERT: D 68 ASN cc_start: 0.7515 (m110) cc_final: 0.7026 (t0) REVERT: D 96 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7128 (p0) REVERT: D 119 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: F 119 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6271 (mmm) REVERT: F 200 TYR cc_start: 0.7021 (m-80) cc_final: 0.6802 (m-80) REVERT: F 244 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: F 382 MET cc_start: 0.6981 (ttm) cc_final: 0.6714 (mtp) outliers start: 25 outliers final: 15 residues processed: 144 average time/residue: 1.4440 time to fit residues: 228.6194 Evaluate side-chains 147 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 244 GLN Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.0060 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097617 restraints weight = 35280.927| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.21 r_work: 0.2976 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15423 Z= 0.187 Angle : 0.509 7.369 20902 Z= 0.268 Chirality : 0.042 0.158 2349 Planarity : 0.005 0.119 2612 Dihedral : 10.304 178.800 2357 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.54 % Allowed : 15.36 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % 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: 0.36 (0.19), residues: 1910 helix: 1.50 (0.18), residues: 866 sheet: -0.46 (0.40), residues: 170 loop : -0.89 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.017 0.001 PHE B 6 TYR 0.016 0.001 TYR D 141 ARG 0.013 0.000 ARG B 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4928.46 seconds wall clock time: 89 minutes 58.06 seconds (5398.06 seconds total)