Starting phenix.real_space_refine on Sun May 18 18:07:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxp_27772/05_2025/8dxp_27772.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxp_27772/05_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_27772/05_2025/8dxp_27772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxp_27772/05_2025/8dxp_27772.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxp_27772/05_2025/8dxp_27772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxp_27772/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 11.16, per 1000 atoms: 0.64 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: 4.87 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: 1.50 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: 4.72 Time building geometry restraints manager: 5.52 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 39.600 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.060 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.710 ------------------------------------------------------------------------------- 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 : 2.114 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: 0.3137 time to fit residues: 157.1736 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 : 2.158 ------------------------------------------------------------------------------- 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 = 0.139878 restraints weight = 28347.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.138370 restraints weight = 25627.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139721 restraints weight = 22840.812| |-----------------------------------------------------------------------------| 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 : 2.020 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: 0.6483 (ttt) REVERT: D 368 ASN cc_start: 0.8333 (m-40) cc_final: 0.7859 (m-40) REVERT: G 356 GLN cc_start: 0.7789 (mp10) cc_final: 0.7479 (mp10) outliers start: 23 outliers final: 16 residues processed: 320 average time/residue: 0.3130 time to fit residues: 146.0888 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 : 1.838 ------------------------------------------------------------------------------- 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: 0.7980 chunk 48 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.173927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135610 restraints weight = 28185.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133954 restraints weight = 23897.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135127 restraints weight = 22285.180| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1888 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= 0.129 Angle : 0.521 10.200 24239 Z= 0.276 Chirality : 0.038 0.162 2643 Planarity : 0.003 0.033 2948 Dihedral : 3.924 26.699 2279 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.91 % Allowed : 13.53 % Favored : 84.56 % 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: 0.67 (0.20), residues: 2055 helix: 1.70 (0.15), residues: 1355 sheet: -0.45 (0.46), residues: 137 loop : -2.57 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 145 HIS 0.007 0.001 HIS B 157 PHE 0.021 0.001 PHE D 41 TYR 0.016 0.001 TYR G 353 ARG 0.006 0.000 ARG E 347 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 1021) hydrogen bonds : angle 3.88360 ( 3024) SS BOND : bond 0.00312 ( 14) SS BOND : angle 0.68468 ( 28) covalent geometry : bond 0.00292 (17934) covalent geometry : angle 0.52036 (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 319 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 2.166 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: B 373 MET cc_start: 0.8045 (ttp) cc_final: 0.7760 (tmm) REVERT: C 48 MET cc_start: 0.6713 (ttp) cc_final: 0.6435 (ttt) REVERT: D 242 PHE cc_start: 0.7229 (m-80) cc_final: 0.7012 (m-80) REVERT: D 259 TYR cc_start: 0.7262 (t80) cc_final: 0.6654 (t80) REVERT: F 398 ASN cc_start: 0.8622 (m-40) cc_final: 0.8415 (m110) REVERT: G 140 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7229 (tp) REVERT: G 356 GLN cc_start: 0.8086 (mp10) cc_final: 0.7879 (mp10) outliers start: 37 outliers final: 26 residues processed: 303 average time/residue: 0.3001 time to fit residues: 134.4961 Evaluate side-chains 285 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 2.9990 chunk 196 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 G 106 GLN G 121 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.177321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141378 restraints weight = 28251.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139181 restraints weight = 37419.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141062 restraints weight = 30276.820| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17948 Z= 0.125 Angle : 0.511 11.648 24239 Z= 0.271 Chirality : 0.038 0.159 2643 Planarity : 0.003 0.033 2948 Dihedral : 3.881 26.721 2279 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.27 % Allowed : 15.50 % Favored : 82.23 % 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: 0.69 (0.20), residues: 2055 helix: 1.71 (0.15), residues: 1357 sheet: -0.43 (0.46), residues: 139 loop : -2.55 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 145 HIS 0.007 0.001 HIS B 157 PHE 0.033 0.001 PHE G 372 TYR 0.015 0.001 TYR C 279 ARG 0.006 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 1021) hydrogen bonds : angle 3.74832 ( 3024) SS BOND : bond 0.00298 ( 14) SS BOND : angle 0.62944 ( 28) covalent geometry : bond 0.00284 (17934) covalent geometry : angle 0.51116 (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 323 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 2.049 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: 0.6935 (tmm) cc_final: 0.6413 (tmm) REVERT: B 373 MET cc_start: 0.7766 (ttp) cc_final: 0.7476 (tmm) REVERT: C 48 MET cc_start: 0.6928 (ttp) cc_final: 0.6637 (ttt) REVERT: D 279 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5226 (t80) REVERT: D 376 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7033 (mtm) REVERT: F 398 ASN cc_start: 0.8592 (m-40) cc_final: 0.7963 (m110) REVERT: G 140 LEU cc_start: 0.7608 (tt) cc_final: 0.7110 (tp) outliers start: 44 outliers final: 32 residues processed: 304 average time/residue: 0.2998 time to fit residues: 135.1509 Evaluate side-chains 298 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 2.043 ------------------------------------------------------------------------------- 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 157 HIS 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 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 265 GLN Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain G residue 40 VAL 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 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: 0.5980 chunk 196 optimal weight: 0.2980 chunk 190 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 ASN E 157 HIS E 265 GLN G 106 GLN G 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.172784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136267 restraints weight = 28258.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134310 restraints weight = 37174.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.135640 restraints weight = 33440.005| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2340 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= 0.147 Angle : 0.532 12.356 24239 Z= 0.281 Chirality : 0.039 0.157 2643 Planarity : 0.003 0.037 2948 Dihedral : 3.933 26.731 2279 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.94 % Allowed : 16.37 % Favored : 80.68 % 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: 0.64 (0.20), residues: 2055 helix: 1.65 (0.15), residues: 1357 sheet: -0.37 (0.46), residues: 137 loop : -2.55 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 145 HIS 0.009 0.001 HIS B 157 PHE 0.028 0.002 PHE G 372 TYR 0.018 0.001 TYR A 330 ARG 0.004 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1021) hydrogen bonds : angle 3.74583 ( 3024) SS BOND : bond 0.00352 ( 14) SS BOND : angle 0.63820 ( 28) covalent geometry : bond 0.00342 (17934) covalent geometry : angle 0.53178 (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 340 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7787 (tt) REVERT: C 48 MET cc_start: 0.7134 (ttp) cc_final: 0.6829 (ttt) REVERT: D 279 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.5490 (t80) REVERT: D 376 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7186 (mtm) REVERT: G 140 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7177 (tp) REVERT: G 248 PHE cc_start: 0.7195 (t80) cc_final: 0.6942 (t80) outliers start: 57 outliers final: 40 residues processed: 320 average time/residue: 0.2912 time to fit residues: 139.6345 Evaluate side-chains 313 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 370 PHE 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 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 295 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 186 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.174632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136790 restraints weight = 28159.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134620 restraints weight = 29775.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136084 restraints weight = 26877.332| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2541 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= 0.118 Angle : 0.522 11.168 24239 Z= 0.274 Chirality : 0.038 0.155 2643 Planarity : 0.003 0.050 2948 Dihedral : 3.876 26.092 2279 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.69 % Allowed : 17.72 % Favored : 79.60 % 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: 0.67 (0.20), residues: 2055 helix: 1.66 (0.15), residues: 1359 sheet: -0.38 (0.46), residues: 139 loop : -2.50 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 145 HIS 0.011 0.001 HIS B 157 PHE 0.030 0.001 PHE G 372 TYR 0.014 0.001 TYR D 259 ARG 0.005 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 1021) hydrogen bonds : angle 3.65114 ( 3024) SS BOND : bond 0.00265 ( 14) SS BOND : angle 0.55839 ( 28) covalent geometry : bond 0.00267 (17934) covalent geometry : angle 0.52237 (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 337 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 1.803 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: 0.6927 (tmm) cc_final: 0.6505 (tmm) REVERT: B 239 LYS cc_start: 0.6805 (mtmm) cc_final: 0.6555 (mtmm) REVERT: C 48 MET cc_start: 0.7114 (ttp) cc_final: 0.6755 (ttt) REVERT: D 279 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.5468 (t80) outliers start: 52 outliers final: 38 residues processed: 316 average time/residue: 0.2873 time to fit residues: 135.5549 Evaluate side-chains 306 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 265 GLN 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 263 VAL Chi-restraints excluded: chain D residue 277 ILE 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 47 VAL Chi-restraints excluded: chain E residue 126 TYR Chi-restraints excluded: chain E residue 335 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 351 PHE Chi-restraints excluded: chain G residue 356 GLN 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: 6.9990 chunk 68 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 62 optimal weight: 0.0980 chunk 150 optimal weight: 0.6980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS F 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.178248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.142145 restraints weight = 28163.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139384 restraints weight = 39983.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141362 restraints weight = 29832.586| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2753 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= 0.111 Angle : 0.532 14.366 24239 Z= 0.275 Chirality : 0.037 0.158 2643 Planarity : 0.003 0.055 2948 Dihedral : 3.827 24.866 2279 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.79 % Allowed : 17.98 % Favored : 79.24 % 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: 1.70 (0.15), residues: 1358 sheet: -0.21 (0.47), residues: 136 loop : -2.52 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 145 HIS 0.011 0.001 HIS B 157 PHE 0.028 0.001 PHE G 372 TYR 0.014 0.001 TYR A 330 ARG 0.007 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 1021) hydrogen bonds : angle 3.60479 ( 3024) SS BOND : bond 0.00244 ( 14) SS BOND : angle 0.52632 ( 28) covalent geometry : bond 0.00248 (17934) covalent geometry : angle 0.53230 (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 339 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 2.022 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: 0.6951 (tmm) cc_final: 0.6572 (tmm) REVERT: B 239 LYS cc_start: 0.6908 (mtmm) cc_final: 0.6586 (mtmm) REVERT: B 373 MET cc_start: 0.7796 (tmm) cc_final: 0.7486 (tmm) REVERT: D 279 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.5479 (t80) REVERT: D 369 ASP cc_start: 0.7299 (p0) cc_final: 0.6986 (t0) REVERT: D 373 MET cc_start: 0.5036 (ptt) cc_final: 0.4748 (ptt) REVERT: E 49 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7998 (tp40) outliers start: 54 outliers final: 45 residues processed: 318 average time/residue: 0.3127 time to fit residues: 149.3223 Evaluate side-chains 316 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET 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 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 241 LEU Chi-restraints excluded: chain D residue 263 VAL 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 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 327 VAL Chi-restraints excluded: chain F residue 375 HIS Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 ASN 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: 0.9980 chunk 69 optimal weight: 0.1980 chunk 179 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 192 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS C 143 ASN D 309 ASN E 112 ASN F 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.175174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.137868 restraints weight = 28060.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135765 restraints weight = 30617.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137397 restraints weight = 25797.998| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2838 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= 0.114 Angle : 0.537 13.090 24239 Z= 0.279 Chirality : 0.038 0.163 2643 Planarity : 0.003 0.064 2948 Dihedral : 3.829 26.924 2279 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.20 % Allowed : 17.92 % Favored : 78.87 % 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: 1.68 (0.15), residues: 1361 sheet: -0.26 (0.46), residues: 139 loop : -2.52 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 145 HIS 0.010 0.001 HIS B 157 PHE 0.035 0.001 PHE B 158 TYR 0.014 0.001 TYR E 353 ARG 0.006 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 1021) hydrogen bonds : angle 3.57283 ( 3024) SS BOND : bond 0.00256 ( 14) SS BOND : angle 0.53593 ( 28) covalent geometry : bond 0.00258 (17934) covalent geometry : angle 0.53689 (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 338 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7107 (mmm-85) cc_final: 0.6902 (tpp80) REVERT: A 373 MET cc_start: 0.6956 (tmm) cc_final: 0.6569 (tmm) REVERT: D 279 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.5497 (t80) REVERT: D 369 ASP cc_start: 0.7391 (p0) cc_final: 0.7109 (t0) REVERT: D 373 MET cc_start: 0.5153 (ptt) cc_final: 0.4839 (ptt) outliers start: 62 outliers final: 53 residues processed: 314 average time/residue: 0.2944 time to fit residues: 137.6154 Evaluate side-chains 324 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 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 C residue 143 ASN 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 132 LEU 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 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 261 MET 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 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 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 132 LEU 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 284 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 200 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 122 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS C 143 ASN ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 ASN F 375 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.175112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139260 restraints weight = 28069.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136229 restraints weight = 41597.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.138177 restraints weight = 33060.220| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2917 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= 0.121 Angle : 0.553 12.735 24239 Z= 0.285 Chirality : 0.038 0.158 2643 Planarity : 0.003 0.057 2948 Dihedral : 3.827 24.741 2279 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.46 % Allowed : 17.61 % Favored : 78.93 % 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: 1.70 (0.15), residues: 1356 sheet: -0.20 (0.46), residues: 138 loop : -2.51 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 145 HIS 0.011 0.001 HIS B 157 PHE 0.035 0.001 PHE G 248 TYR 0.014 0.001 TYR E 353 ARG 0.006 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 1021) hydrogen bonds : angle 3.59028 ( 3024) SS BOND : bond 0.00282 ( 14) SS BOND : angle 0.54140 ( 28) covalent geometry : bond 0.00276 (17934) covalent geometry : angle 0.55288 (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 339 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 272 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7158 (mmm-85) cc_final: 0.6949 (tpp80) REVERT: A 373 MET cc_start: 0.6845 (tmm) cc_final: 0.6637 (tmm) REVERT: C 373 MET cc_start: 0.8597 (mmm) cc_final: 0.8202 (mmm) REVERT: D 279 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5531 (t80) REVERT: D 373 MET cc_start: 0.5161 (ptt) cc_final: 0.4832 (ptt) REVERT: E 347 ARG cc_start: 0.5870 (mmm160) cc_final: 0.5493 (tpp-160) outliers start: 67 outliers final: 57 residues processed: 314 average time/residue: 0.2824 time to fit residues: 133.6824 Evaluate side-chains 325 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 1.902 ------------------------------------------------------------------------------- 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 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 143 ASN 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 297 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 132 LEU 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 37 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 126 TYR 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 33 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 157 HIS Chi-restraints excluded: chain G residue 166 PHE Chi-restraints excluded: chain G residue 279 TYR Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 0.6980 chunk 202 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS C 143 ASN ** E 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS F 375 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140416 restraints weight = 27955.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138216 restraints weight = 36445.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139894 restraints weight = 29195.602| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2971 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= 0.117 Angle : 0.548 12.326 24239 Z= 0.287 Chirality : 0.038 0.159 2643 Planarity : 0.003 0.050 2948 Dihedral : 3.838 27.094 2279 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.94 % Allowed : 18.44 % Favored : 78.62 % 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: 0.73 (0.20), residues: 2055 helix: 1.71 (0.15), residues: 1355 sheet: -0.14 (0.46), residues: 138 loop : -2.51 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 145 HIS 0.011 0.001 HIS B 157 PHE 0.029 0.001 PHE B 158 TYR 0.014 0.001 TYR E 353 ARG 0.012 0.000 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 1021) hydrogen bonds : angle 3.58894 ( 3024) SS BOND : bond 0.00261 ( 14) SS BOND : angle 0.52484 ( 28) covalent geometry : bond 0.00263 (17934) covalent geometry : angle 0.54795 (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 325 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7750 (tt) REVERT: C 373 MET cc_start: 0.8651 (mmm) cc_final: 0.8276 (mmm) REVERT: D 279 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.5499 (t80) outliers start: 57 outliers final: 51 residues processed: 306 average time/residue: 0.2985 time to fit residues: 137.1373 Evaluate side-chains 316 residues out of total 1936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 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 132 LEU Chi-restraints excluded: chain C residue 143 ASN 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 D residue 38 ILE Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 132 LEU 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 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 F residue 375 HIS 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 284 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 351 PHE Chi-restraints excluded: chain G residue 356 GLN Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 109 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS C 143 ASN E 112 ASN F 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.178393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.140466 restraints weight = 28698.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.139855 restraints weight = 17252.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140693 restraints weight = 15883.847| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17948 Z= 0.209 Angle : 0.639 12.270 24239 Z= 0.336 Chirality : 0.042 0.156 2643 Planarity : 0.004 0.075 2948 Dihedral : 4.082 27.268 2279 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.10 % Allowed : 18.60 % Favored : 78.31 % 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: 0.43 (0.19), residues: 2055 helix: 1.46 (0.14), residues: 1361 sheet: -0.35 (0.46), residues: 138 loop : -2.60 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 145 HIS 0.011 0.001 HIS B 157 PHE 0.029 0.002 PHE B 158 TYR 0.023 0.002 TYR A 330 ARG 0.014 0.001 ARG D 355 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 1021) hydrogen bonds : angle 3.87570 ( 3024) SS BOND : bond 0.00468 ( 14) SS BOND : angle 0.79730 ( 28) covalent geometry : bond 0.00496 (17934) covalent geometry : angle 0.63921 (24211) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5053.54 seconds wall clock time: 89 minutes 57.36 seconds (5397.36 seconds total)