Starting phenix.real_space_refine on Sun Jun 15 12:02:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxp_27772/06_2025/8dxp_27772.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxp_27772/06_2025/8dxp_27772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dxp_27772/06_2025/8dxp_27772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxp_27772/06_2025/8dxp_27772.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxp_27772/06_2025/8dxp_27772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxp_27772/06_2025/8dxp_27772.cif" } resolution = 3.7 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= -0.001 sd= 0.026 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: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 11541 2.51 5 N 2756 2.21 5 O 3021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17465 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2501 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "D" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2481 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Chain: "E" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2498 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Chain: "F" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2507 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Chain: "G" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2490 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain breaks: 2 Time building chain proxies: 10.17, per 1000 atoms: 0.58 Number of scatterers: 17465 At special positions: 0 Unit cell: (125.4, 117.7, 134.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 3021 8.00 N 2756 7.00 C 11541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.03 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 293 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4054 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 7 sheets defined 71.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 22 through 45 Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 122 through 142 removed outlier: 3.510A pdb=" N TYR A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 151 through 167 removed outlier: 4.084A pdb=" N ILE A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 176 removed outlier: 4.070A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 258 through 283 removed outlier: 3.728A pdb=" N TYR A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 344 removed outlier: 4.262A pdb=" N ARG A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 367 through 378 Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.621A pdb=" N PHE A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 4.173A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.624A pdb=" N VAL B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 47 removed outlier: 5.080A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.621A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 120 " --> pdb=" O TYR B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.886A pdb=" N LYS B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 126' Processing helix chain 'B' and resid 126 through 143 removed outlier: 3.701A pdb=" N ASN B 143 " --> pdb=" O MET B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 165 removed outlier: 4.050A pdb=" N ILE B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.290A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 259 through 283 removed outlier: 3.521A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.559A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 367 through 378 removed outlier: 3.504A pdb=" N ALA B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 393 through 405 removed outlier: 4.133A pdb=" N GLU B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.614A pdb=" N VAL C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 4.193A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.759A pdb=" N LYS C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 126 " --> pdb=" O TRP C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 126' Processing helix chain 'C' and resid 126 through 144 Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 169 through 176 Processing helix chain 'C' and resid 232 through 253 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 284 through 287 removed outlier: 3.556A pdb=" N VAL C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 313 through 343 removed outlier: 3.526A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 removed outlier: 3.589A pdb=" N ARG C 355 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.595A pdb=" N ALA C 371 " --> pdb=" O LYS C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.129A pdb=" N PHE C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 49 removed outlier: 3.611A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 31 " --> pdb=" O PHE D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.730A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.639A pdb=" N LYS D 125 " --> pdb=" O HIS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 142 removed outlier: 3.879A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 167 removed outlier: 3.734A pdb=" N SER D 153 " --> pdb=" O PRO D 149 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 4.316A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.667A pdb=" N LYS D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 282 removed outlier: 3.918A pdb=" N MET D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEU D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 315 through 344 removed outlier: 4.332A pdb=" N ARG D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 359 removed outlier: 3.608A pdb=" N ARG D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 378 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.094A pdb=" N PHE D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 4.018A pdb=" N GLU D 397 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.652A pdb=" N VAL E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 120 removed outlier: 3.843A pdb=" N TYR E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG E 118 " --> pdb=" O MET E 114 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU E 120 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 142 removed outlier: 3.501A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 167 removed outlier: 3.605A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 176 Processing helix chain 'E' and resid 232 through 253 removed outlier: 3.516A pdb=" N GLU E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 283 removed outlier: 3.937A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 removed outlier: 3.998A pdb=" N VAL E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 287' Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.798A pdb=" N PHE E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 removed outlier: 3.846A pdb=" N ARG E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.778A pdb=" N PHE E 372 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET E 373 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP E 381 " --> pdb=" O ILE E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 391 removed outlier: 4.139A pdb=" N PHE E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 405 Processing helix chain 'F' and resid 22 through 25 Processing helix chain 'F' and resid 26 through 49 Processing helix chain 'F' and resid 106 through 120 removed outlier: 4.236A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 143 removed outlier: 3.693A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 167 removed outlier: 4.188A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 3.833A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 253 removed outlier: 3.730A pdb=" N LEU F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 283 removed outlier: 4.663A pdb=" N TYR F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL F 263 " --> pdb=" O TYR F 259 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 342 Processing helix chain 'F' and resid 351 through 359 removed outlier: 3.526A pdb=" N ARG F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 379 removed outlier: 3.593A pdb=" N PHE F 372 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP F 378 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN F 379 " --> pdb=" O HIS F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.084A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 405 removed outlier: 3.688A pdb=" N LEU F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 49 removed outlier: 3.860A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.621A pdb=" N TYR G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.793A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 143 removed outlier: 3.741A pdb=" N ASN G 143 " --> pdb=" O MET G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 148 removed outlier: 4.097A pdb=" N PHE G 148 " --> pdb=" O TRP G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 167 removed outlier: 3.557A pdb=" N ASP G 167 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.928A pdb=" N SER G 176 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU G 177 " --> pdb=" O ARG G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 253 removed outlier: 3.626A pdb=" N ALA G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 245 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 253 " --> pdb=" O ARG G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 281 removed outlier: 3.626A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 302 Processing helix chain 'G' and resid 313 through 341 Processing helix chain 'G' and resid 352 through 357 Processing helix chain 'G' and resid 368 through 379 removed outlier: 4.019A pdb=" N PHE G 372 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN G 379 " --> pdb=" O HIS G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 389 removed outlier: 3.884A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 392 No H-bonds generated for 'chain 'G' and resid 390 through 392' Processing helix chain 'G' and resid 393 through 405 removed outlier: 3.715A pdb=" N GLU G 397 " --> pdb=" O SER G 393 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 56 removed outlier: 3.551A pdb=" N ILE D 53 " --> pdb=" O ASN D 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.645A pdb=" N CYS F 308 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.817A pdb=" N ILE G 53 " --> pdb=" O ASN G 309 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN G 309 " --> pdb=" O ILE G 53 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 3024 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: 4.79 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5178 1.34 - 1.46: 3268 1.46 - 1.57: 9264 1.57 - 1.69: 0 1.69 - 1.81: 224 Bond restraints: 17934 Sorted by residual: bond pdb=" N ASN F 368 " pdb=" CA ASN F 368 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" C ASP C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.50e+00 bond pdb=" N PRO D 382 " pdb=" CA PRO D 382 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.37e+00 bond pdb=" CB LYS C 246 " pdb=" CG LYS C 246 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA ASN F 368 " pdb=" CB ASN F 368 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.69e-02 3.50e+03 9.09e-01 ... (remaining 17929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 23860 1.87 - 3.74: 312 3.74 - 5.62: 36 5.62 - 7.49: 1 7.49 - 9.36: 2 Bond angle restraints: 24211 Sorted by residual: angle pdb=" N TRP C 145 " pdb=" CA TRP C 145 " pdb=" C TRP C 145 " ideal model delta sigma weight residual 114.56 109.93 4.63 1.27e+00 6.20e-01 1.33e+01 angle pdb=" CB LYS C 246 " pdb=" CG LYS C 246 " pdb=" CD LYS C 246 " ideal model delta sigma weight residual 111.30 118.88 -7.58 2.30e+00 1.89e-01 1.09e+01 angle pdb=" N LYS F 367 " pdb=" CA LYS F 367 " pdb=" C LYS F 367 " ideal model delta sigma weight residual 108.34 112.28 -3.94 1.31e+00 5.83e-01 9.03e+00 angle pdb=" C ASN G 368 " pdb=" CA ASN G 368 " pdb=" CB ASN G 368 " ideal model delta sigma weight residual 110.42 116.08 -5.66 1.99e+00 2.53e-01 8.08e+00 angle pdb=" CA TRP B 145 " pdb=" CB TRP B 145 " pdb=" CG TRP B 145 " ideal model delta sigma weight residual 113.60 118.77 -5.17 1.90e+00 2.77e-01 7.40e+00 ... (remaining 24206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9386 17.97 - 35.94: 983 35.94 - 53.91: 159 53.91 - 71.88: 16 71.88 - 89.85: 14 Dihedral angle restraints: 10558 sinusoidal: 4295 harmonic: 6263 Sorted by residual: dihedral pdb=" CA ASP B 25 " pdb=" C ASP B 25 " pdb=" N VAL B 26 " pdb=" CA VAL B 26 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU B 117 " pdb=" C GLU B 117 " pdb=" N ARG B 118 " pdb=" CA ARG B 118 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLU F 117 " pdb=" C GLU F 117 " pdb=" N ARG F 118 " pdb=" CA ARG F 118 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 10555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1735 0.030 - 0.060: 667 0.060 - 0.090: 163 0.090 - 0.119: 67 0.119 - 0.149: 11 Chirality restraints: 2643 Sorted by residual: chirality pdb=" CA ILE G 363 " pdb=" N ILE G 363 " pdb=" C ILE G 363 " pdb=" CB ILE G 363 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE C 53 " pdb=" N ILE C 53 " pdb=" C ILE C 53 " pdb=" CB ILE C 53 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE B 363 " pdb=" N ILE B 363 " pdb=" C ILE B 363 " pdb=" CB ILE B 363 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2640 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 145 " 0.023 2.00e-02 2.50e+03 1.51e-02 5.73e+00 pdb=" CG TRP B 145 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 145 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 145 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 145 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 145 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 145 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 145 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 145 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 242 " 0.008 2.00e-02 2.50e+03 1.15e-02 2.31e+00 pdb=" CG PHE F 242 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE F 242 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE F 242 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 242 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE F 242 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE F 242 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 260 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ALA C 260 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA C 260 " -0.009 2.00e-02 2.50e+03 pdb=" N MET C 261 " -0.008 2.00e-02 2.50e+03 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4181 2.79 - 3.31: 17199 3.31 - 3.84: 27513 3.84 - 4.37: 30137 4.37 - 4.90: 52493 Nonbonded interactions: 131523 Sorted by model distance: nonbonded pdb=" NE2 HIS F 134 " pdb=" OH TYR F 279 " model vdw 2.258 3.120 nonbonded pdb=" O GLU G 352 " pdb=" OE1 GLN G 356 " model vdw 2.266 3.040 nonbonded pdb=" ND1 HIS F 314 " pdb=" OE2 GLU G 117 " model vdw 2.271 3.120 nonbonded pdb=" NH2 ARG A 58 " pdb=" OE1 GLU G 95 " model vdw 2.301 3.120 nonbonded pdb=" O ASN F 280 " pdb=" ND2 ASN F 280 " model vdw 2.303 3.120 ... (remaining 131518 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'B' and (resid 16 through 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'C' and (resid 16 through 59 or resid 96 through 175 or resid 234 through \ 405)) selection = (chain 'D' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'E' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'F' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'G' and (resid 16 through 59 or resid 96 through 175 or resid 177 or resi \ d 235 through 405)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.190 Find NCS groups from input model: 1.020 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.003 0.047 17948 Z= 0.131 Angle : 0.553 9.361 24239 Z= 0.312 Chirality : 0.035 0.149 2643 Planarity : 0.003 0.031 2948 Dihedral : 14.487 89.846 6462 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.20), residues: 2055 helix: 1.76 (0.15), residues: 1304 sheet: -0.98 (0.48), residues: 119 loop : -2.54 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 145 HIS 0.008 0.001 HIS B 134 PHE 0.026 0.001 PHE F 242 TYR 0.019 0.001 TYR A 279 ARG 0.004 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.15052 ( 1021) hydrogen bonds : angle 5.65929 ( 3024) SS BOND : bond 0.00244 ( 14) SS BOND : angle 0.47281 ( 28) covalent geometry : bond 0.00273 (17934) covalent geometry : angle 0.55316 (24211) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.7578 (mtm) cc_final: 0.7215 (mtm) REVERT: G 356 GLN cc_start: 0.7399 (mp10) cc_final: 0.7110 (mp10) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3118 time to fit residues: 157.3115 Evaluate side-chains 268 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 87 optimal weight: 0.0040 chunk 53 optimal weight: 0.0040 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.5806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS B 49 GLN B 157 HIS B 251 HIS C 106 GLN C 251 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS E 265 GLN E 309 ASN E 314 HIS E 398 ASN F 280 ASN F 398 ASN G 314 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.176972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139881 restraints weight = 28347.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138367 restraints weight = 25637.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139722 restraints weight = 22843.373| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17948 Z= 0.131 Angle : 0.556 11.506 24239 Z= 0.292 Chirality : 0.039 0.156 2643 Planarity : 0.003 0.049 2948 Dihedral : 4.037 26.432 2279 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.19 % Allowed : 10.54 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.20), residues: 2055 helix: 1.76 (0.15), residues: 1350 sheet: -0.59 (0.45), residues: 139 loop : -2.57 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 145 HIS 0.008 0.001 HIS E 157 PHE 0.055 0.002 PHE E 242 TYR 0.016 0.001 TYR F 279 ARG 0.004 0.000 ARG D 249 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 1021) hydrogen bonds : angle 4.11151 ( 3024) SS BOND : bond 0.00348 ( 14) SS BOND : angle 0.92346 ( 28) covalent geometry : bond 0.00284 (17934) covalent geometry : angle 0.55496 (24211) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 308 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.6727 (ttp) cc_final: 0.6482 (ttt) REVERT: D 368 ASN cc_start: 0.8333 (m-40) cc_final: 0.7859 (m-40) REVERT: G 356 GLN cc_start: 0.7790 (mp10) cc_final: 0.7479 (mp10) outliers start: 23 outliers final: 16 residues processed: 320 average time/residue: 0.3303 time to fit residues: 155.7811 Evaluate side-chains 288 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 163 optimal weight: 0.0470 chunk 48 optimal weight: 0.5980 chunk 199 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 251 HIS E 157 HIS F 398 ASN G 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.176902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139073 restraints weight = 28134.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136968 restraints weight = 27350.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.138308 restraints weight = 24234.917| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17948 Z= 0.110 Angle : 0.505 10.176 24239 Z= 0.267 Chirality : 0.037 0.163 2643 Planarity : 0.003 0.034 2948 Dihedral : 3.878 26.244 2279 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.60 % Allowed : 13.12 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.20), residues: 2055 helix: 1.77 (0.15), residues: 1350 sheet: -0.40 (0.46), residues: 137 loop : -2.53 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 145 HIS 0.007 0.001 HIS B 157 PHE 0.021 0.001 PHE F 391 TYR 0.015 0.001 TYR G 353 ARG 0.006 0.000 ARG E 347 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 1021) hydrogen bonds : angle 3.82065 ( 3024) SS BOND : bond 0.00246 ( 14) SS BOND : angle 0.65624 ( 28) covalent geometry : bond 0.00235 (17934) covalent geometry : angle 0.50496 (24211) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.6614 (ttp) cc_final: 0.6342 (ttt) REVERT: C 114 MET cc_start: 0.7362 (ttm) cc_final: 0.6957 (ttp) REVERT: D 242 PHE cc_start: 0.7036 (m-80) cc_final: 0.6774 (m-80) REVERT: D 259 TYR cc_start: 0.7212 (t80) cc_final: 0.6641 (t80) REVERT: G 356 GLN cc_start: 0.8046 (mp10) cc_final: 0.7695 (mp10) outliers start: 31 outliers final: 23 residues processed: 306 average time/residue: 0.3342 time to fit residues: 153.2321 Evaluate side-chains 289 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 266 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 166 PHE Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 80 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 203 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 HIS E 157 HIS F 251 HIS F 398 ASN G 106 GLN G 121 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.178593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141332 restraints weight = 28069.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138536 restraints weight = 28767.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140129 restraints weight = 23572.575| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17948 Z= 0.118 Angle : 0.502 10.500 24239 Z= 0.267 Chirality : 0.037 0.157 2643 Planarity : 0.003 0.033 2948 Dihedral : 3.824 26.368 2279 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.07 % Allowed : 15.03 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.20), residues: 2055 helix: 1.77 (0.15), residues: 1347 sheet: -0.41 (0.46), residues: 139 loop : -2.52 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 145 HIS 0.011 0.001 HIS F 251 PHE 0.030 0.001 PHE G 372 TYR 0.015 0.001 TYR C 279 ARG 0.003 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 1021) hydrogen bonds : angle 3.70979 ( 3024) SS BOND : bond 0.00279 ( 14) SS BOND : angle 0.61518 ( 28) covalent geometry : bond 0.00265 (17934) covalent geometry : angle 0.50156 (24211) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6908 (tmm) cc_final: 0.6408 (tmm) REVERT: B 373 MET cc_start: 0.7543 (tmm) cc_final: 0.7253 (tmm) REVERT: C 48 MET cc_start: 0.6798 (ttp) cc_final: 0.6527 (ttt) REVERT: C 392 LEU cc_start: 0.7152 (tp) cc_final: 0.6800 (mm) REVERT: D 279 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5258 (t80) REVERT: D 376 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6909 (mtm) REVERT: G 140 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7225 (tp) REVERT: G 356 GLN cc_start: 0.8083 (mp10) cc_final: 0.7807 (mp10) outliers start: 40 outliers final: 27 residues processed: 301 average time/residue: 0.2983 time to fit residues: 133.9859 Evaluate side-chains 294 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 166 PHE Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 196 optimal weight: 0.0270 chunk 190 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 ASN E 134 HIS E 157 HIS F 251 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141569 restraints weight = 28474.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138590 restraints weight = 39113.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140704 restraints weight = 32248.309| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17948 Z= 0.119 Angle : 0.502 11.309 24239 Z= 0.264 Chirality : 0.037 0.155 2643 Planarity : 0.003 0.036 2948 Dihedral : 3.818 26.295 2279 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.53 % Allowed : 15.91 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.20), residues: 2055 helix: 1.73 (0.15), residues: 1356 sheet: -0.39 (0.47), residues: 139 loop : -2.49 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 145 HIS 0.009 0.001 HIS B 157 PHE 0.028 0.001 PHE G 372 TYR 0.015 0.001 TYR D 259 ARG 0.005 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 1021) hydrogen bonds : angle 3.63919 ( 3024) SS BOND : bond 0.00278 ( 14) SS BOND : angle 0.56984 ( 28) covalent geometry : bond 0.00270 (17934) covalent geometry : angle 0.50207 (24211) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 282 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6971 (tmm) cc_final: 0.6479 (tmm) REVERT: C 48 MET cc_start: 0.6990 (ttp) cc_final: 0.6706 (ttt) REVERT: D 242 PHE cc_start: 0.6998 (m-80) cc_final: 0.6774 (m-80) REVERT: D 279 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5313 (t80) REVERT: D 376 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7124 (mtm) REVERT: G 140 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7232 (tp) REVERT: G 248 PHE cc_start: 0.7248 (t80) cc_final: 0.5912 (t80) outliers start: 49 outliers final: 36 residues processed: 313 average time/residue: 0.2866 time to fit residues: 135.2310 Evaluate side-chains 300 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS E 265 GLN F 251 HIS F 375 HIS F 398 ASN G 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.174625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137666 restraints weight = 28305.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135421 restraints weight = 31913.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137020 restraints weight = 27752.766| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17948 Z= 0.175 Angle : 0.564 12.846 24239 Z= 0.300 Chirality : 0.040 0.156 2643 Planarity : 0.003 0.061 2948 Dihedral : 3.953 26.482 2279 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.25 % Allowed : 16.79 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.20), residues: 2055 helix: 1.55 (0.15), residues: 1357 sheet: -0.34 (0.46), residues: 136 loop : -2.52 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 145 HIS 0.011 0.001 HIS F 251 PHE 0.033 0.002 PHE G 372 TYR 0.032 0.002 TYR B 380 ARG 0.004 0.000 ARG E 347 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 1021) hydrogen bonds : angle 3.82613 ( 3024) SS BOND : bond 0.00406 ( 14) SS BOND : angle 0.69063 ( 28) covalent geometry : bond 0.00413 (17934) covalent geometry : angle 0.56362 (24211) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 LYS cc_start: 0.6747 (mtmm) cc_final: 0.6471 (mtmm) REVERT: D 279 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.5475 (t80) REVERT: D 369 ASP cc_start: 0.7306 (p0) cc_final: 0.6843 (t70) REVERT: D 376 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7082 (mtm) REVERT: E 347 ARG cc_start: 0.5913 (mmm160) cc_final: 0.5706 (tpp-160) REVERT: E 356 GLN cc_start: 0.6658 (mp10) cc_final: 0.6438 (mp10) REVERT: G 140 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7246 (tp) outliers start: 63 outliers final: 47 residues processed: 318 average time/residue: 0.3096 time to fit residues: 149.4823 Evaluate side-chains 315 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 265 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 145 TRP Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 375 HIS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 119 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.173763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137499 restraints weight = 27893.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134444 restraints weight = 39070.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136307 restraints weight = 32457.477| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17948 Z= 0.125 Angle : 0.551 14.606 24239 Z= 0.284 Chirality : 0.038 0.155 2643 Planarity : 0.003 0.040 2948 Dihedral : 3.918 25.583 2279 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.63 % Allowed : 18.29 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.20), residues: 2055 helix: 1.62 (0.15), residues: 1354 sheet: -0.31 (0.46), residues: 136 loop : -2.50 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP C 145 HIS 0.011 0.001 HIS F 375 PHE 0.032 0.001 PHE G 372 TYR 0.020 0.001 TYR B 380 ARG 0.006 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 1021) hydrogen bonds : angle 3.69536 ( 3024) SS BOND : bond 0.00293 ( 14) SS BOND : angle 0.58204 ( 28) covalent geometry : bond 0.00285 (17934) covalent geometry : angle 0.55077 (24211) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 281 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6943 (tmm) cc_final: 0.6592 (tmm) REVERT: B 239 LYS cc_start: 0.6890 (mtmm) cc_final: 0.6577 (mtmm) REVERT: D 279 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.5419 (t80) REVERT: D 369 ASP cc_start: 0.7323 (p0) cc_final: 0.6887 (t0) REVERT: D 373 MET cc_start: 0.5871 (ptt) cc_final: 0.5597 (ptt) REVERT: G 140 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7400 (tp) outliers start: 51 outliers final: 42 residues processed: 314 average time/residue: 0.3510 time to fit residues: 168.7102 Evaluate side-chains 309 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 121 optimal weight: 0.7980 chunk 192 optimal weight: 0.3980 chunk 83 optimal weight: 0.0020 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS C 112 ASN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.179092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141705 restraints weight = 28448.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138979 restraints weight = 32792.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.141023 restraints weight = 26918.646| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17948 Z= 0.107 Angle : 0.526 13.493 24239 Z= 0.272 Chirality : 0.037 0.163 2643 Planarity : 0.003 0.032 2948 Dihedral : 3.824 26.197 2279 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.58 % Allowed : 18.23 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.20), residues: 2055 helix: 1.71 (0.15), residues: 1355 sheet: -0.32 (0.46), residues: 138 loop : -2.50 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 145 HIS 0.012 0.001 HIS B 157 PHE 0.029 0.001 PHE G 372 TYR 0.016 0.001 TYR D 259 ARG 0.008 0.000 ARG E 347 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 1021) hydrogen bonds : angle 3.56481 ( 3024) SS BOND : bond 0.00226 ( 14) SS BOND : angle 0.51132 ( 28) covalent geometry : bond 0.00233 (17934) covalent geometry : angle 0.52628 (24211) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.6901 (tmm) cc_final: 0.6489 (tmm) REVERT: D 166 PHE cc_start: 0.4346 (OUTLIER) cc_final: 0.3590 (t80) REVERT: D 279 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.5569 (t80) REVERT: D 369 ASP cc_start: 0.7333 (p0) cc_final: 0.7112 (t0) REVERT: F 242 PHE cc_start: 0.7525 (m-80) cc_final: 0.7188 (m-10) outliers start: 50 outliers final: 41 residues processed: 315 average time/residue: 0.3012 time to fit residues: 142.5507 Evaluate side-chains 316 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 146 PHE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 200 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.177068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140453 restraints weight = 28334.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.138349 restraints weight = 31053.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139857 restraints weight = 27166.037| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17948 Z= 0.126 Angle : 0.550 12.844 24239 Z= 0.286 Chirality : 0.038 0.170 2643 Planarity : 0.003 0.032 2948 Dihedral : 3.838 27.760 2279 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.84 % Allowed : 18.18 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.20), residues: 2055 helix: 1.66 (0.15), residues: 1355 sheet: -0.32 (0.46), residues: 138 loop : -2.54 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 145 HIS 0.012 0.001 HIS F 251 PHE 0.061 0.001 PHE E 242 TYR 0.016 0.001 TYR A 330 ARG 0.006 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 1021) hydrogen bonds : angle 3.59743 ( 3024) SS BOND : bond 0.00290 ( 14) SS BOND : angle 0.57688 ( 28) covalent geometry : bond 0.00288 (17934) covalent geometry : angle 0.54976 (24211) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8184 (pt0) cc_final: 0.7974 (pt0) REVERT: A 311 THR cc_start: 0.7992 (p) cc_final: 0.7748 (p) REVERT: A 373 MET cc_start: 0.6996 (tmm) cc_final: 0.6598 (tmm) REVERT: D 166 PHE cc_start: 0.4188 (OUTLIER) cc_final: 0.3351 (t80) REVERT: D 279 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.5484 (t80) REVERT: F 242 PHE cc_start: 0.7515 (m-80) cc_final: 0.7187 (m-10) REVERT: F 251 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7068 (t70) outliers start: 55 outliers final: 48 residues processed: 311 average time/residue: 0.3047 time to fit residues: 143.6848 Evaluate side-chains 320 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 146 PHE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 312 MET Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 248 PHE Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 0.9980 chunk 202 optimal weight: 0.0980 chunk 63 optimal weight: 0.0070 chunk 7 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 205 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS E 112 ASN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 ASN F 106 GLN F 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.179233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141081 restraints weight = 28227.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139451 restraints weight = 20928.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140895 restraints weight = 20670.003| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17948 Z= 0.108 Angle : 0.539 12.618 24239 Z= 0.282 Chirality : 0.038 0.163 2643 Planarity : 0.003 0.049 2948 Dihedral : 3.820 26.906 2279 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.69 % Allowed : 18.75 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.20), residues: 2055 helix: 1.72 (0.15), residues: 1351 sheet: -0.21 (0.46), residues: 138 loop : -2.55 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 145 HIS 0.012 0.001 HIS B 157 PHE 0.061 0.001 PHE E 242 TYR 0.016 0.001 TYR D 259 ARG 0.010 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 1021) hydrogen bonds : angle 3.54322 ( 3024) SS BOND : bond 0.00229 ( 14) SS BOND : angle 0.50416 ( 28) covalent geometry : bond 0.00237 (17934) covalent geometry : angle 0.53883 (24211) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8235 (pt0) REVERT: A 311 THR cc_start: 0.8058 (p) cc_final: 0.7815 (p) REVERT: A 373 MET cc_start: 0.6676 (tmm) cc_final: 0.6395 (tmm) REVERT: B 239 LYS cc_start: 0.6696 (mtmm) cc_final: 0.6434 (mtmm) REVERT: D 166 PHE cc_start: 0.4125 (OUTLIER) cc_final: 0.3330 (t80) REVERT: D 279 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.5620 (t80) REVERT: F 242 PHE cc_start: 0.7615 (m-80) cc_final: 0.7304 (m-10) outliers start: 52 outliers final: 45 residues processed: 307 average time/residue: 0.3091 time to fit residues: 144.3577 Evaluate side-chains 319 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 279 TYR Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 334 CYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 165 CYS Chi-restraints excluded: chain F residue 265 GLN Chi-restraints excluded: chain F residue 279 TYR Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 chunk 145 optimal weight: 0.0010 chunk 6 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN E 112 ASN ** E 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.184830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147922 restraints weight = 28412.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.144746 restraints weight = 20597.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.145954 restraints weight = 16333.404| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17948 Z= 0.109 Angle : 0.544 12.187 24239 Z= 0.283 Chirality : 0.038 0.165 2643 Planarity : 0.003 0.043 2948 Dihedral : 3.809 26.919 2279 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.84 % Allowed : 19.01 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.20), residues: 2055 helix: 1.73 (0.15), residues: 1346 sheet: -0.20 (0.47), residues: 138 loop : -2.56 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 145 HIS 0.012 0.001 HIS B 157 PHE 0.060 0.001 PHE E 242 TYR 0.015 0.001 TYR D 259 ARG 0.011 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 1021) hydrogen bonds : angle 3.53538 ( 3024) SS BOND : bond 0.00225 ( 14) SS BOND : angle 0.47622 ( 28) covalent geometry : bond 0.00240 (17934) covalent geometry : angle 0.54378 (24211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5499.16 seconds wall clock time: 97 minutes 45.65 seconds (5865.65 seconds total)