Starting phenix.real_space_refine on Sun Sep 13 22:42:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9usv_64472/09_2026/9usv_64472.cif Found real_map, /net/cci-nas-00/data/ceres_data/9usv_64472/09_2026/9usv_64472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9usv_64472/09_2026/9usv_64472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9usv_64472/09_2026/9usv_64472.map" model { file = "/net/cci-nas-00/data/ceres_data/9usv_64472/09_2026/9usv_64472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9usv_64472/09_2026/9usv_64472.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 74 5.16 5 C 16278 2.51 5 N 4138 2.21 5 O 4970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25460 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 4298 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Chain: "D" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "E" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "A" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 4216 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 530, 4216 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "C" Number of atoms: 4298 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 541, 4298 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 25, 'TRANS': 515} Chain breaks: 2 Time building chain proxies: 4.99, per 1000 atoms: 0.20 Number of scatterers: 25460 At special positions: 0 Unit cell: (119.7, 172.9, 114.38, 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 74 16.00 O 4970 8.00 N 4138 7.00 C 16278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6104 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 68 sheets defined 19.1% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.791A pdb=" N LEU F 9 " --> pdb=" O ILE F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 112 through 120 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.919A pdb=" N VAL F 164 " --> pdb=" O PRO F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 206 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.829A pdb=" N ASP F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP F 294 " --> pdb=" O ARG F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 395 removed outlier: 3.638A pdb=" N THR F 393 " --> pdb=" O ASN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 419 Processing helix chain 'F' and resid 458 through 469 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 186 through 189 Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.917A pdb=" N ASP D 293 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 389 through 395 Processing helix chain 'D' and resid 396 through 401 removed outlier: 3.987A pdb=" N TRP D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 401' Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 112 through 120 Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 186 through 189 Processing helix chain 'E' and resid 198 through 206 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.981A pdb=" N ASP E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 395 removed outlier: 3.644A pdb=" N THR E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 removed outlier: 3.955A pdb=" N TRP E 400 " --> pdb=" O PRO E 396 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR E 401 " --> pdb=" O VAL E 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 396 through 401' Processing helix chain 'E' and resid 413 through 418 Processing helix chain 'E' and resid 458 through 469 Processing helix chain 'E' and resid 516 through 521 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.687A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.835A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.633A pdb=" N THR A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.096A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.777A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.675A pdb=" N THR B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.641A pdb=" N SER B 402 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 2 through 9 removed outlier: 3.715A pdb=" N LEU C 9 " --> pdb=" O ILE C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.816A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 363 Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.646A pdb=" N THR C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.584A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'F' and resid 32 through 40 removed outlier: 4.136A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL F 219 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR F 64 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU F 69 " --> pdb=" O ILE F 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 32 through 40 removed outlier: 4.136A pdb=" N ILE F 215 " --> pdb=" O HIS F 68 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N HIS F 68 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR F 217 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU F 66 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL F 219 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR F 64 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 42 through 44 removed outlier: 6.115A pdb=" N SER F 102 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.565A pdb=" N VAL F 78 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 139 through 141 removed outlier: 6.191A pdb=" N ARG F 83 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG F 193 " --> pdb=" O PHE F 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 227 through 239 removed outlier: 4.684A pdb=" N LEU F 525 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE F 239 " --> pdb=" O LYS F 523 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS F 523 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN F 522 " --> pdb=" O TYR F 262 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA F 252 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.637A pdb=" N ARG F 475 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA F 252 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU F 532 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER F 254 " --> pdb=" O ASN F 530 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN F 522 " --> pdb=" O TYR F 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 243 through 246 removed outlier: 6.578A pdb=" N SER F 504 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL F 445 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG F 506 " --> pdb=" O LEU F 443 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU F 443 " --> pdb=" O ARG F 506 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL F 508 " --> pdb=" O SER F 441 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU F 443 " --> pdb=" O SER F 454 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER F 454 " --> pdb=" O LEU F 443 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL F 445 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 450 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 296 through 299 Processing sheet with id=AB1, first strand: chain 'F' and resid 320 through 323 removed outlier: 6.700A pdb=" N ASP F 327 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE F 368 " --> pdb=" O ASP F 327 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR F 329 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLY F 370 " --> pdb=" O TYR F 329 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS F 331 " --> pdb=" O GLY F 370 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR F 372 " --> pdb=" O LYS F 331 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP F 333 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE F 365 " --> pdb=" O HIS F 386 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS F 386 " --> pdb=" O PHE F 365 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA F 367 " --> pdb=" O ILE F 384 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE F 384 " --> pdb=" O ALA F 367 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR F 369 " --> pdb=" O ALA F 382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 349 through 350 Processing sheet with id=AB3, first strand: chain 'D' and resid 32 through 40 removed outlier: 3.541A pdb=" N MET D 218 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU D 69 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D 152 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 32 through 40 removed outlier: 3.541A pdb=" N MET D 218 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 215 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS D 68 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR D 217 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU D 66 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.108A pdb=" N SER D 102 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 78 through 79 removed outlier: 6.607A pdb=" N VAL D 78 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 140 Processing sheet with id=AB8, first strand: chain 'D' and resid 227 through 236 removed outlier: 3.858A pdb=" N GLN D 522 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA D 252 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 475 through 478 removed outlier: 7.058A pdb=" N ALA D 252 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 532 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER D 254 " --> pdb=" O ASN D 530 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN D 522 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 243 through 246 removed outlier: 6.939A pdb=" N LEU D 443 " --> pdb=" O SER D 454 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER D 454 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 445 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 269 through 270 Processing sheet with id=AC3, first strand: chain 'D' and resid 296 through 299 Processing sheet with id=AC4, first strand: chain 'D' and resid 320 through 323 removed outlier: 7.940A pdb=" N ILE D 368 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR D 329 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLY D 370 " --> pdb=" O TYR D 329 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS D 331 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR D 372 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASP D 333 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA D 367 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE D 384 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR D 369 " --> pdb=" O ALA D 382 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG D 378 " --> pdb=" O SER D 373 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 349 through 350 Processing sheet with id=AC6, first strand: chain 'E' and resid 34 through 40 removed outlier: 4.294A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU E 69 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 34 through 40 removed outlier: 4.294A pdb=" N ILE E 215 " --> pdb=" O HIS E 68 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N HIS E 68 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR E 217 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU E 66 " --> pdb=" O TYR E 217 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 78 through 79 removed outlier: 6.620A pdb=" N VAL E 78 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 139 through 141 Processing sheet with id=AD2, first strand: chain 'E' and resid 227 through 236 removed outlier: 3.596A pdb=" N SER E 227 " --> pdb=" O VAL E 535 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU E 532 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA E 252 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA E 252 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 475 through 478 removed outlier: 3.533A pdb=" N ARG E 475 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA E 252 " --> pdb=" O LEU E 532 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU E 532 " --> pdb=" O ALA E 252 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER E 254 " --> pdb=" O ASN E 530 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN E 522 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 243 through 246 removed outlier: 6.903A pdb=" N LEU E 443 " --> pdb=" O SER E 454 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER E 454 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 445 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 269 through 270 Processing sheet with id=AD6, first strand: chain 'E' and resid 296 through 299 Processing sheet with id=AD7, first strand: chain 'E' and resid 320 through 323 removed outlier: 6.410A pdb=" N ASP E 327 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE E 368 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N TYR E 329 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLY E 370 " --> pdb=" O TYR E 329 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS E 331 " --> pdb=" O GLY E 370 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N TYR E 372 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP E 333 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE E 365 " --> pdb=" O HIS E 386 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS E 386 " --> pdb=" O PHE E 365 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA E 367 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE E 384 " --> pdb=" O ALA E 367 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR E 369 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 378 " --> pdb=" O SER E 373 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 349 through 350 Processing sheet with id=AD9, first strand: chain 'A' and resid 32 through 39 removed outlier: 4.341A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 32 through 39 removed outlier: 4.341A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.650A pdb=" N THR A 179 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 100 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A 181 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 98 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 183 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.546A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 139 through 141 removed outlier: 3.793A pdb=" N GLY A 82 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 227 through 236 removed outlier: 3.549A pdb=" N ASP A 531 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN A 524 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 259 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 526 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 257 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 528 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 255 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A 530 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA A 251 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.169A pdb=" N ALA A 251 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A 530 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 255 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 528 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 257 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 526 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 259 " --> pdb=" O GLN A 524 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN A 524 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.782A pdb=" N ARG A 442 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AE9, first strand: chain 'A' and resid 296 through 299 removed outlier: 3.634A pdb=" N SER A 299 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 340 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.858A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AF3, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.571A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 152 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.571A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 42 through 44 removed outlier: 5.904A pdb=" N SER B 102 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 78 through 79 removed outlier: 7.152A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 139 through 140 removed outlier: 5.705A pdb=" N ARG B 83 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 193 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 227 through 239 removed outlier: 4.737A pdb=" N LEU B 525 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE B 239 " --> pdb=" O LYS B 523 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS B 523 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 475 through 478 removed outlier: 6.839A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.548A pdb=" N ARG B 442 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 443 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER B 454 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 445 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 450 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 296 through 299 removed outlier: 3.586A pdb=" N LEU B 343 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 313 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.649A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS B 383 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B 371 " --> pdb=" O PHE B 381 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE B 381 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 373 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR B 379 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AG5, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.752A pdb=" N MET C 218 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.752A pdb=" N MET C 218 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 42 through 44 removed outlier: 5.997A pdb=" N SER C 102 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.740A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 139 through 141 removed outlier: 6.294A pdb=" N ARG C 83 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 227 through 239 removed outlier: 3.533A pdb=" N SER C 227 " --> pdb=" O VAL C 535 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU C 525 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE C 239 " --> pdb=" O LYS C 523 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS C 523 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.617A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 243 through 247 removed outlier: 6.141A pdb=" N LYS C 502 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE C 447 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER C 504 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL C 445 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG C 506 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU C 443 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 508 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 296 through 299 removed outlier: 3.502A pdb=" N SER C 340 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.534A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS C 383 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR C 371 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE C 381 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER C 373 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N THR C 379 " --> pdb=" O SER C 373 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2604 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: 5.19 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7793 1.33 - 1.45: 3795 1.45 - 1.57: 14298 1.57 - 1.69: 0 1.69 - 1.81: 124 Bond restraints: 26010 Sorted by residual: bond pdb=" C ASN E 203 " pdb=" N LYS E 204 " ideal model delta sigma weight residual 1.335 1.385 -0.049 1.34e-02 5.57e+03 1.35e+01 bond pdb=" C ASP F 432 " pdb=" N PHE F 433 " ideal model delta sigma weight residual 1.335 1.287 0.048 1.36e-02 5.41e+03 1.24e+01 bond pdb=" N GLY B 80 " pdb=" CA GLY B 80 " ideal model delta sigma weight residual 1.447 1.475 -0.028 9.20e-03 1.18e+04 9.22e+00 bond pdb=" C GLY D 301 " pdb=" N PRO D 302 " ideal model delta sigma weight residual 1.329 1.362 -0.032 1.18e-02 7.18e+03 7.52e+00 bond pdb=" N ILE F 431 " pdb=" CA ILE F 431 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.37e-02 5.33e+03 6.99e+00 ... (remaining 26005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 34839 1.64 - 3.28: 475 3.28 - 4.92: 49 4.92 - 6.57: 12 6.57 - 8.21: 3 Bond angle restraints: 35378 Sorted by residual: angle pdb=" CA GLY B 80 " pdb=" C GLY B 80 " pdb=" O GLY B 80 " ideal model delta sigma weight residual 121.48 118.00 3.48 9.90e-01 1.02e+00 1.23e+01 angle pdb=" O ASN E 203 " pdb=" C ASN E 203 " pdb=" N LYS E 204 " ideal model delta sigma weight residual 122.15 125.95 -3.80 1.14e+00 7.69e-01 1.11e+01 angle pdb=" CB LYS F 354 " pdb=" CG LYS F 354 " pdb=" CD LYS F 354 " ideal model delta sigma weight residual 111.30 118.51 -7.21 2.30e+00 1.89e-01 9.82e+00 angle pdb=" CA ASP F 432 " pdb=" C ASP F 432 " pdb=" O ASP F 432 " ideal model delta sigma weight residual 121.58 118.12 3.46 1.16e+00 7.43e-01 8.87e+00 angle pdb=" O THR C 143 " pdb=" C THR C 143 " pdb=" N PRO C 144 " ideal model delta sigma weight residual 121.55 119.23 2.32 7.80e-01 1.64e+00 8.83e+00 ... (remaining 35373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13757 17.94 - 35.88: 1508 35.88 - 53.82: 290 53.82 - 71.75: 59 71.75 - 89.69: 22 Dihedral angle restraints: 15636 sinusoidal: 6152 harmonic: 9484 Sorted by residual: dihedral pdb=" CA ILE F 323 " pdb=" C ILE F 323 " pdb=" N GLN F 324 " pdb=" CA GLN F 324 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA MET C 349 " pdb=" C MET C 349 " pdb=" N PHE C 350 " pdb=" CA PHE C 350 " ideal model delta harmonic sigma weight residual 180.00 162.42 17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP A 501 " pdb=" CB ASP A 501 " pdb=" CG ASP A 501 " pdb=" OD1 ASP A 501 " ideal model delta sinusoidal sigma weight residual -30.00 -89.24 59.24 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 15633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2834 0.039 - 0.078: 754 0.078 - 0.117: 454 0.117 - 0.156: 43 0.156 - 0.195: 3 Chirality restraints: 4088 Sorted by residual: chirality pdb=" CB ILE C 323 " pdb=" CA ILE C 323 " pdb=" CG1 ILE C 323 " pdb=" CG2 ILE C 323 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA ILE F 431 " pdb=" N ILE F 431 " pdb=" C ILE F 431 " pdb=" CB ILE F 431 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA ASN B 346 " pdb=" N ASN B 346 " pdb=" C ASN B 346 " pdb=" CB ASN B 346 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 4085 not shown) Planarity restraints: 4514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 301 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 302 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 306 " 0.035 5.00e-02 4.00e+02 5.42e-02 4.69e+00 pdb=" N PRO B 307 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 404 " -0.178 9.50e-02 1.11e+02 8.00e-02 3.98e+00 pdb=" NE ARG E 404 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG E 404 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG E 404 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 404 " -0.005 2.00e-02 2.50e+03 ... (remaining 4511 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 829 2.71 - 3.26: 24628 3.26 - 3.80: 40087 3.80 - 4.35: 51261 4.35 - 4.90: 89188 Nonbonded interactions: 205993 Sorted by model distance: nonbonded pdb=" OH TYR C 157 " pdb=" OD2 ASP C 163 " model vdw 2.162 3.040 nonbonded pdb=" OH TYR E 453 " pdb=" OE1 GLU E 455 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR E 352 " pdb=" OD1 ASN E 515 " model vdw 2.244 3.040 nonbonded pdb=" N GLU C 111 " pdb=" OE1 GLU C 111 " model vdw 2.252 3.120 nonbonded pdb=" OH TYR B 453 " pdb=" OE1 GLU B 455 " model vdw 2.254 3.040 ... (remaining 205988 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 15 through 547) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 15 through 547) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.67 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.750 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 0.049 26010 Z= 0.136 Angle : 0.494 8.207 35378 Z= 0.277 Chirality : 0.046 0.195 4088 Planarity : 0.004 0.080 4514 Dihedral : 15.469 89.692 9532 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 18.86 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 3174 helix: 0.12 (0.25), residues: 488 sheet: 0.98 (0.17), residues: 926 loop : -0.01 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 193 TYR 0.018 0.001 TYR F 32 PHE 0.024 0.001 BPHE A 357 TRP 0.006 0.001 TRP B 108 HIS 0.006 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (26010) covalent geometry : angle 0.49352 / 0.28 (35378) hydrogen bonds : bond 0.19669 / 13.07 ( 886) hydrogen bonds : angle 8.41459 / 5.85 ( 2604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 198 ASP cc_start: 0.7604 (t0) cc_final: 0.7347 (t0) REVERT: F 404 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7925 (tpp80) REVERT: D 484 LYS cc_start: 0.8364 (mmtp) cc_final: 0.8073 (mmtm) REVERT: E 198 ASP cc_start: 0.7346 (t0) cc_final: 0.6626 (p0) REVERT: A 353 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7713 (tpp-160) REVERT: A 539 GLN cc_start: 0.6576 (tm-30) cc_final: 0.6370 (tm-30) REVERT: B 81 MET cc_start: 0.5890 (ttt) cc_final: 0.5671 (ttp) REVERT: C 81 MET cc_start: 0.8216 (mtm) cc_final: 0.7924 (mpp) REVERT: C 339 MET cc_start: 0.8388 (tpt) cc_final: 0.7990 (tpt) REVERT: C 531 ASP cc_start: 0.8633 (m-30) cc_final: 0.7613 (p0) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1657 time to fit residues: 85.9456 Evaluate side-chains 304 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 ASN B 223 GLN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107254 restraints weight = 34305.563| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.67 r_work: 0.3152 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26010 Z= 0.143 Angle : 0.480 6.321 35378 Z= 0.258 Chirality : 0.047 0.163 4088 Planarity : 0.004 0.052 4514 Dihedral : 3.639 14.467 3488 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.73 % Allowed : 17.71 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.15), residues: 3174 helix: 0.08 (0.25), residues: 490 sheet: 0.78 (0.17), residues: 904 loop : 0.10 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 404 TYR 0.012 0.001 TYR F 62 PHE 0.016 0.001 PHE B 214 TRP 0.005 0.001 TRP B 108 HIS 0.005 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (26010) covalent geometry : angle 0.48029 / 0.26 (35378) hydrogen bonds : bond 0.03950 / 2.60 ( 886) hydrogen bonds : angle 5.75300 / 3.99 ( 2604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 323 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 404 ARG cc_start: 0.8350 (tpp80) cc_final: 0.7691 (mtm180) REVERT: F 416 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8244 (t) REVERT: D 33 MET cc_start: 0.8988 (tpp) cc_final: 0.8780 (tpp) REVERT: E 27 GLN cc_start: 0.8282 (mp10) cc_final: 0.7812 (mp10) REVERT: E 198 ASP cc_start: 0.7838 (t0) cc_final: 0.6905 (p0) REVERT: E 204 LYS cc_start: 0.9158 (tttt) cc_final: 0.8692 (mmmt) REVERT: A 349 MET cc_start: 0.8176 (ptt) cc_final: 0.7817 (ptp) REVERT: B 81 MET cc_start: 0.5611 (ttt) cc_final: 0.5230 (tmm) REVERT: B 223 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7162 (mm-40) REVERT: B 267 ASP cc_start: 0.8166 (t0) cc_final: 0.7915 (t0) REVERT: B 446 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7516 (mtp85) REVERT: C 531 ASP cc_start: 0.8862 (m-30) cc_final: 0.7223 (p0) outliers start: 51 outliers final: 38 residues processed: 350 average time/residue: 0.1642 time to fit residues: 93.0102 Evaluate side-chains 330 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 291 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 416 SER Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 284 optimal weight: 3.9990 chunk 251 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 344 HIS D 386 HIS A 250 HIS ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102749 restraints weight = 34968.525| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.72 r_work: 0.3071 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 26010 Z= 0.296 Angle : 0.574 7.913 35378 Z= 0.305 Chirality : 0.051 0.158 4088 Planarity : 0.004 0.066 4514 Dihedral : 4.233 15.801 3488 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.95 % Allowed : 17.88 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.15), residues: 3174 helix: -0.25 (0.24), residues: 498 sheet: 0.36 (0.17), residues: 898 loop : -0.16 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 193 TYR 0.017 0.002 TYR F 62 PHE 0.023 0.002 PHE B 199 TRP 0.011 0.002 TRP B 108 HIS 0.007 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.30 (26010) covalent geometry : angle 0.57405 / 0.31 (35378) hydrogen bonds : bond 0.04223 / 2.76 ( 886) hydrogen bonds : angle 5.68859 / 3.93 ( 2604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 304 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 198 ASP cc_start: 0.7965 (t0) cc_final: 0.7577 (t0) REVERT: F 282 ASP cc_start: 0.8147 (m-30) cc_final: 0.7938 (m-30) REVERT: F 353 ARG cc_start: 0.7335 (mtt90) cc_final: 0.6911 (mtp-110) REVERT: F 404 ARG cc_start: 0.8382 (tpp80) cc_final: 0.7919 (tpp80) REVERT: E 198 ASP cc_start: 0.8033 (t0) cc_final: 0.7030 (p0) REVERT: E 204 LYS cc_start: 0.9128 (tttt) cc_final: 0.8711 (mmmt) REVERT: A 50 ASN cc_start: 0.7908 (t0) cc_final: 0.7644 (t0) REVERT: A 74 GLU cc_start: 0.8578 (pm20) cc_final: 0.8332 (pm20) REVERT: A 114 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8547 (mm-30) REVERT: A 349 MET cc_start: 0.8224 (ptt) cc_final: 0.7877 (ptp) REVERT: A 353 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7729 (tpp-160) REVERT: A 484 LYS cc_start: 0.8384 (mmtp) cc_final: 0.7968 (tppt) REVERT: B 31 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8174 (mt) REVERT: B 81 MET cc_start: 0.5630 (ttt) cc_final: 0.5259 (tmm) REVERT: B 90 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8437 (m) REVERT: B 223 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7167 (mm-40) REVERT: B 267 ASP cc_start: 0.8579 (t0) cc_final: 0.8257 (t0) REVERT: B 436 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7812 (ttmm) REVERT: B 446 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7740 (mtp85) REVERT: C 81 MET cc_start: 0.8613 (mtm) cc_final: 0.7879 (mpp) REVERT: C 278 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8595 (mm-40) REVERT: C 385 SER cc_start: 0.7715 (m) cc_final: 0.7198 (t) REVERT: C 502 LYS cc_start: 0.7363 (pttm) cc_final: 0.7139 (pttm) REVERT: C 531 ASP cc_start: 0.8882 (m-30) cc_final: 0.7292 (p0) outliers start: 87 outliers final: 60 residues processed: 367 average time/residue: 0.1587 time to fit residues: 93.3427 Evaluate side-chains 351 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 288 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 529 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 546 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 167 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 128 HIS E 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106890 restraints weight = 34338.484| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.73 r_work: 0.3125 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26010 Z= 0.119 Angle : 0.455 6.619 35378 Z= 0.244 Chirality : 0.047 0.155 4088 Planarity : 0.004 0.052 4514 Dihedral : 3.845 15.987 3488 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.93 % Allowed : 19.50 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3174 helix: -0.05 (0.24), residues: 490 sheet: 0.36 (0.17), residues: 924 loop : -0.02 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 404 TYR 0.012 0.001 TYR F 32 PHE 0.023 0.001 PHE B 199 TRP 0.006 0.001 TRP B 108 HIS 0.005 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (26010) covalent geometry : angle 0.45468 / 0.24 (35378) hydrogen bonds : bond 0.03222 / 2.11 ( 886) hydrogen bonds : angle 5.23005 / 3.62 ( 2604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 325 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 230 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8276 (mm-30) REVERT: F 282 ASP cc_start: 0.7912 (m-30) cc_final: 0.7712 (m-30) REVERT: F 353 ARG cc_start: 0.7278 (mtt90) cc_final: 0.6962 (mtp-110) REVERT: F 404 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7750 (tpp80) REVERT: D 280 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7796 (mm-30) REVERT: E 198 ASP cc_start: 0.7737 (t0) cc_final: 0.6848 (p0) REVERT: E 204 LYS cc_start: 0.9119 (tttt) cc_final: 0.8706 (mmmt) REVERT: A 50 ASN cc_start: 0.7722 (t0) cc_final: 0.7402 (t0) REVERT: A 114 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 230 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 349 MET cc_start: 0.8208 (ptt) cc_final: 0.7840 (ptp) REVERT: A 353 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7770 (tpp-160) REVERT: A 357 PHE cc_start: 0.7507 (t80) cc_final: 0.6892 (t80) REVERT: A 484 LYS cc_start: 0.8327 (mmtp) cc_final: 0.7962 (tppt) REVERT: B 81 MET cc_start: 0.5697 (ttt) cc_final: 0.5277 (tmm) REVERT: B 223 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7128 (mm-40) REVERT: B 267 ASP cc_start: 0.8542 (t0) cc_final: 0.8249 (t0) REVERT: B 436 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7608 (ttmm) REVERT: B 446 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7709 (mtp85) REVERT: C 81 MET cc_start: 0.8622 (mtm) cc_final: 0.7784 (mpp) REVERT: C 218 MET cc_start: 0.8106 (mtt) cc_final: 0.7901 (mtt) REVERT: C 385 SER cc_start: 0.7576 (m) cc_final: 0.7045 (t) REVERT: C 531 ASP cc_start: 0.8690 (m-30) cc_final: 0.7118 (p0) REVERT: C 534 LYS cc_start: 0.7977 (ttmm) cc_final: 0.7639 (ttpt) outliers start: 57 outliers final: 44 residues processed: 364 average time/residue: 0.1773 time to fit residues: 102.1319 Evaluate side-chains 345 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 42 optimal weight: 0.0270 chunk 35 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 313 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 177 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 240 ASN D 515 ASN E 145 ASN A 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105371 restraints weight = 34413.683| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.75 r_work: 0.3123 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26010 Z= 0.128 Angle : 0.451 6.889 35378 Z= 0.240 Chirality : 0.047 0.153 4088 Planarity : 0.004 0.053 4514 Dihedral : 3.746 15.588 3488 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.34 % Allowed : 19.13 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3174 helix: -0.07 (0.24), residues: 506 sheet: 0.32 (0.17), residues: 924 loop : -0.03 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 488 TYR 0.013 0.001 TYR E 258 PHE 0.022 0.001 PHE B 199 TRP 0.005 0.001 TRP B 108 HIS 0.004 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (26010) covalent geometry : angle 0.45060 / 0.24 (35378) hydrogen bonds : bond 0.03125 / 2.04 ( 886) hydrogen bonds : angle 5.05025 / 3.49 ( 2604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 326 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 198 ASP cc_start: 0.7643 (t0) cc_final: 0.7345 (t0) REVERT: F 230 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8281 (mm-30) REVERT: F 353 ARG cc_start: 0.7258 (mtt90) cc_final: 0.6939 (mtp-110) REVERT: F 404 ARG cc_start: 0.8322 (tpp80) cc_final: 0.7830 (tpp80) REVERT: F 436 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8137 (tttt) REVERT: D 230 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8392 (mt-10) REVERT: D 280 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7822 (mm-30) REVERT: D 425 ASP cc_start: 0.8719 (t0) cc_final: 0.8451 (t70) REVERT: D 436 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7931 (ttpp) REVERT: E 198 ASP cc_start: 0.7697 (t0) cc_final: 0.6879 (p0) REVERT: E 204 LYS cc_start: 0.9113 (tttt) cc_final: 0.8718 (mmmt) REVERT: A 50 ASN cc_start: 0.7727 (t0) cc_final: 0.7392 (t0) REVERT: A 134 GLU cc_start: 0.8929 (mp0) cc_final: 0.8548 (tm-30) REVERT: A 230 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8142 (mt-10) REVERT: A 349 MET cc_start: 0.8205 (ptt) cc_final: 0.7849 (ptp) REVERT: A 357 PHE cc_start: 0.7378 (t80) cc_final: 0.6752 (t80) REVERT: A 484 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7968 (tppt) REVERT: B 81 MET cc_start: 0.5425 (ttt) cc_final: 0.4956 (tmm) REVERT: B 223 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7129 (mm-40) REVERT: B 267 ASP cc_start: 0.8530 (t0) cc_final: 0.8220 (t0) REVERT: B 436 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7493 (ttmm) REVERT: B 446 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7739 (mtp85) REVERT: C 57 GLU cc_start: 0.8059 (tt0) cc_final: 0.7443 (tt0) REVERT: C 81 MET cc_start: 0.8516 (mtm) cc_final: 0.7723 (mpp) REVERT: C 109 GLU cc_start: 0.8935 (pt0) cc_final: 0.8526 (mt-10) REVERT: C 175 ASP cc_start: 0.8487 (m-30) cc_final: 0.8122 (m-30) REVERT: C 218 MET cc_start: 0.8118 (mtt) cc_final: 0.7874 (mtt) REVERT: C 385 SER cc_start: 0.7440 (m) cc_final: 0.6986 (t) REVERT: C 531 ASP cc_start: 0.8669 (m-30) cc_final: 0.7131 (p0) REVERT: C 534 LYS cc_start: 0.7992 (ttmm) cc_final: 0.7722 (ttpt) outliers start: 69 outliers final: 56 residues processed: 374 average time/residue: 0.1569 time to fit residues: 94.2457 Evaluate side-chains 358 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 300 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 339 MET Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 269 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 280 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 145 ASN C 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106683 restraints weight = 34395.927| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.74 r_work: 0.3122 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26010 Z= 0.138 Angle : 0.456 7.213 35378 Z= 0.243 Chirality : 0.047 0.153 4088 Planarity : 0.004 0.052 4514 Dihedral : 3.732 14.738 3488 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.61 % Allowed : 19.23 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3174 helix: -0.08 (0.24), residues: 506 sheet: 0.26 (0.17), residues: 924 loop : -0.04 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 353 TYR 0.011 0.001 TYR D 258 PHE 0.023 0.001 PHE B 199 TRP 0.005 0.001 TRP F 108 HIS 0.007 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (26010) covalent geometry : angle 0.45552 / 0.24 (35378) hydrogen bonds : bond 0.03102 / 2.03 ( 886) hydrogen bonds : angle 5.00563 / 3.45 ( 2604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 320 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 113 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: F 198 ASP cc_start: 0.7671 (t0) cc_final: 0.7371 (t0) REVERT: F 230 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8285 (mm-30) REVERT: F 353 ARG cc_start: 0.7200 (mtt90) cc_final: 0.6971 (mtp-110) REVERT: F 404 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7823 (tpp80) REVERT: D 230 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8348 (mt-10) REVERT: D 280 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7827 (mm-30) REVERT: D 425 ASP cc_start: 0.8715 (t0) cc_final: 0.8441 (t70) REVERT: D 436 LYS cc_start: 0.8306 (ttpt) cc_final: 0.7972 (ttpp) REVERT: E 198 ASP cc_start: 0.7692 (t0) cc_final: 0.6883 (p0) REVERT: E 204 LYS cc_start: 0.9126 (tttt) cc_final: 0.8723 (mmmt) REVERT: A 50 ASN cc_start: 0.7720 (t0) cc_final: 0.7390 (t0) REVERT: A 74 GLU cc_start: 0.8345 (pm20) cc_final: 0.8115 (pm20) REVERT: A 177 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8285 (ttmt) REVERT: A 220 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8177 (mtpt) REVERT: A 230 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8155 (mt-10) REVERT: A 349 MET cc_start: 0.8196 (ptt) cc_final: 0.7949 (ptp) REVERT: A 353 ARG cc_start: 0.8127 (tpp-160) cc_final: 0.7787 (tpp-160) REVERT: A 374 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.6610 (t0) REVERT: A 484 LYS cc_start: 0.8313 (mmtp) cc_final: 0.7959 (tppt) REVERT: B 81 MET cc_start: 0.5389 (ttt) cc_final: 0.5039 (tmm) REVERT: B 193 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6135 (ptp90) REVERT: B 223 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7095 (mm-40) REVERT: B 267 ASP cc_start: 0.8552 (t0) cc_final: 0.8221 (t0) REVERT: B 436 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7473 (ttmm) REVERT: B 446 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7791 (mtp85) REVERT: B 471 ASN cc_start: 0.8239 (m110) cc_final: 0.7969 (m110) REVERT: C 35 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: C 57 GLU cc_start: 0.8062 (tt0) cc_final: 0.7443 (tt0) REVERT: C 81 MET cc_start: 0.8505 (mtm) cc_final: 0.7696 (mpp) REVERT: C 109 GLU cc_start: 0.8894 (pt0) cc_final: 0.8289 (mt-10) REVERT: C 175 ASP cc_start: 0.8579 (m-30) cc_final: 0.8170 (m-30) REVERT: C 218 MET cc_start: 0.8122 (mtt) cc_final: 0.7763 (mtt) REVERT: C 385 SER cc_start: 0.7417 (m) cc_final: 0.6963 (t) REVERT: C 524 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6320 (mt0) REVERT: C 534 LYS cc_start: 0.8078 (ttmm) cc_final: 0.7732 (ttpt) outliers start: 77 outliers final: 65 residues processed: 373 average time/residue: 0.1711 time to fit residues: 101.8376 Evaluate side-chains 372 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 278 GLN Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 GLN Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 544 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 225 optimal weight: 0.0980 chunk 189 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 145 ASN C 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.131589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102875 restraints weight = 34786.446| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.05 r_work: 0.3088 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26010 Z= 0.105 Angle : 0.444 7.247 35378 Z= 0.236 Chirality : 0.046 0.154 4088 Planarity : 0.004 0.052 4514 Dihedral : 3.628 14.455 3488 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.44 % Allowed : 19.81 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3174 helix: 0.03 (0.24), residues: 490 sheet: 0.32 (0.17), residues: 918 loop : 0.04 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.011 0.001 TYR D 258 PHE 0.023 0.001 PHE B 199 TRP 0.006 0.001 TRP F 108 HIS 0.005 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (26010) covalent geometry : angle 0.44378 / 0.24 (35378) hydrogen bonds : bond 0.02913 / 1.90 ( 886) hydrogen bonds : angle 4.87864 / 3.36 ( 2604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 319 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 113 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.7265 (tp30) REVERT: F 198 ASP cc_start: 0.7694 (t0) cc_final: 0.7392 (t0) REVERT: F 230 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8360 (mm-30) REVERT: F 404 ARG cc_start: 0.8343 (tpp80) cc_final: 0.7876 (tpp80) REVERT: F 436 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8174 (tttt) REVERT: F 506 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7748 (ttt90) REVERT: D 74 GLU cc_start: 0.8278 (mp0) cc_final: 0.7824 (mp0) REVERT: D 230 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8422 (mt-10) REVERT: D 280 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7962 (mm-30) REVERT: D 436 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8064 (ttpp) REVERT: D 498 ARG cc_start: 0.7480 (mmm-85) cc_final: 0.7101 (mmm-85) REVERT: E 17 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7071 (ptpp) REVERT: E 198 ASP cc_start: 0.7592 (t0) cc_final: 0.6884 (p0) REVERT: E 204 LYS cc_start: 0.9136 (tttt) cc_final: 0.8851 (mmmt) REVERT: E 455 GLU cc_start: 0.8066 (pt0) cc_final: 0.7854 (pt0) REVERT: A 50 ASN cc_start: 0.7658 (t0) cc_final: 0.7295 (t0) REVERT: A 220 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8264 (mtpt) REVERT: A 230 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8066 (mt-10) REVERT: A 349 MET cc_start: 0.8146 (ptt) cc_final: 0.7877 (ptp) REVERT: A 374 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.6584 (t0) REVERT: A 484 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7999 (tppt) REVERT: B 81 MET cc_start: 0.5709 (ttt) cc_final: 0.5336 (tmm) REVERT: B 193 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6121 (ptp90) REVERT: B 223 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7260 (mm-40) REVERT: B 267 ASP cc_start: 0.8595 (t0) cc_final: 0.8295 (t0) REVERT: B 446 ARG cc_start: 0.8471 (mtp85) cc_final: 0.7404 (mtp85) REVERT: B 471 ASN cc_start: 0.8261 (m110) cc_final: 0.7980 (m110) REVERT: C 35 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: C 57 GLU cc_start: 0.8118 (tt0) cc_final: 0.7577 (tt0) REVERT: C 109 GLU cc_start: 0.8887 (pt0) cc_final: 0.8409 (mt-10) REVERT: C 175 ASP cc_start: 0.8495 (m-30) cc_final: 0.8126 (m-30) REVERT: C 218 MET cc_start: 0.8196 (mtt) cc_final: 0.7844 (mtt) REVERT: C 339 MET cc_start: 0.7903 (tpt) cc_final: 0.7660 (tpt) REVERT: C 385 SER cc_start: 0.7603 (m) cc_final: 0.7171 (t) REVERT: C 524 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6527 (mt0) REVERT: C 534 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7953 (ttpt) outliers start: 72 outliers final: 54 residues processed: 370 average time/residue: 0.1706 time to fit residues: 99.6091 Evaluate side-chains 360 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 506 ARG Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 273 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 206 optimal weight: 0.0040 chunk 15 optimal weight: 0.6980 chunk 236 optimal weight: 0.9980 chunk 277 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 145 ASN A 515 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104151 restraints weight = 34745.521| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.05 r_work: 0.3106 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26010 Z= 0.095 Angle : 0.436 7.180 35378 Z= 0.233 Chirality : 0.046 0.158 4088 Planarity : 0.004 0.060 4514 Dihedral : 3.512 14.620 3488 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.27 % Allowed : 20.12 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3174 helix: 0.10 (0.25), residues: 490 sheet: 0.37 (0.17), residues: 926 loop : 0.08 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 353 TYR 0.014 0.001 TYR B 62 PHE 0.019 0.001 PHE B 199 TRP 0.009 0.001 TRP F 108 HIS 0.005 0.001 HIS E 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 (26010) covalent geometry : angle 0.43649 / 0.23 (35378) hydrogen bonds : bond 0.02774 / 1.82 ( 886) hydrogen bonds : angle 4.73806 / 3.27 ( 2604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 113 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: F 198 ASP cc_start: 0.7650 (t0) cc_final: 0.7367 (t0) REVERT: F 230 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8373 (mm-30) REVERT: F 404 ARG cc_start: 0.8358 (tpp80) cc_final: 0.7900 (tpp80) REVERT: F 436 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8227 (tttt) REVERT: F 506 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7733 (ttt90) REVERT: D 74 GLU cc_start: 0.8305 (mp0) cc_final: 0.7951 (mp0) REVERT: D 230 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8360 (mt-10) REVERT: D 241 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8630 (mm-40) REVERT: D 280 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7968 (mm-30) REVERT: D 383 HIS cc_start: 0.8044 (t70) cc_final: 0.7799 (t70) REVERT: D 436 LYS cc_start: 0.8363 (ttpt) cc_final: 0.7939 (ttpp) REVERT: D 498 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.7146 (mmm-85) REVERT: E 17 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7069 (ptpp) REVERT: E 198 ASP cc_start: 0.7539 (t0) cc_final: 0.6732 (p0) REVERT: E 204 LYS cc_start: 0.9148 (tttt) cc_final: 0.8868 (mmmt) REVERT: A 50 ASN cc_start: 0.7686 (t0) cc_final: 0.7286 (t0) REVERT: A 74 GLU cc_start: 0.8336 (pm20) cc_final: 0.8061 (pm20) REVERT: A 114 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8088 (mm-30) REVERT: A 220 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8175 (mtpt) REVERT: A 349 MET cc_start: 0.8131 (ptt) cc_final: 0.7868 (ptp) REVERT: B 81 MET cc_start: 0.5457 (ttt) cc_final: 0.5155 (tmm) REVERT: B 193 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6050 (ptp90) REVERT: B 223 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7187 (mm-40) REVERT: B 267 ASP cc_start: 0.8563 (t0) cc_final: 0.8248 (t0) REVERT: B 436 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7488 (ttmm) REVERT: B 446 ARG cc_start: 0.8427 (mtp85) cc_final: 0.7841 (mtp85) REVERT: C 35 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8306 (pt0) REVERT: C 57 GLU cc_start: 0.8118 (tt0) cc_final: 0.7518 (tt0) REVERT: C 81 MET cc_start: 0.8637 (mtm) cc_final: 0.7943 (mpp) REVERT: C 109 GLU cc_start: 0.8943 (pt0) cc_final: 0.8464 (mt-10) REVERT: C 218 MET cc_start: 0.8175 (mtt) cc_final: 0.7798 (mtt) REVERT: C 385 SER cc_start: 0.7441 (m) cc_final: 0.7017 (t) REVERT: C 524 GLN cc_start: 0.6819 (OUTLIER) cc_final: 0.6531 (mt0) REVERT: C 534 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7952 (ttpt) outliers start: 67 outliers final: 52 residues processed: 363 average time/residue: 0.1702 time to fit residues: 98.0260 Evaluate side-chains 356 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 296 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 506 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 35 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 524 GLN Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 285 optimal weight: 4.9990 chunk 301 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 315 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 383 HIS E 145 ASN A 515 ASN B 268 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098111 restraints weight = 35466.102| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.01 r_work: 0.3023 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 26010 Z= 0.292 Angle : 0.572 8.304 35378 Z= 0.302 Chirality : 0.051 0.205 4088 Planarity : 0.004 0.068 4514 Dihedral : 4.085 15.590 3488 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.75 % Allowed : 19.91 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 3174 helix: -0.26 (0.24), residues: 504 sheet: 0.11 (0.17), residues: 892 loop : -0.13 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 404 TYR 0.023 0.002 TYR F 463 PHE 0.030 0.002 PHE B 199 TRP 0.010 0.002 TRP A 108 HIS 0.005 0.001 HIS E 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.29 (26010) covalent geometry : angle 0.57183 / 0.30 (35378) hydrogen bonds : bond 0.03731 / 2.43 ( 886) hydrogen bonds : angle 5.26376 / 3.62 ( 2604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 301 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 113 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: F 134 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7748 (tm-30) REVERT: F 198 ASP cc_start: 0.7916 (t0) cc_final: 0.7536 (t0) REVERT: F 204 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8326 (tttt) REVERT: F 230 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8351 (mm-30) REVERT: F 404 ARG cc_start: 0.8418 (tpp80) cc_final: 0.7952 (tpp80) REVERT: F 506 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7825 (ttt90) REVERT: D 436 LYS cc_start: 0.8380 (ttpt) cc_final: 0.8064 (ttpp) REVERT: E 17 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7268 (ptpp) REVERT: E 198 ASP cc_start: 0.7717 (t0) cc_final: 0.6974 (p0) REVERT: E 204 LYS cc_start: 0.9156 (tttt) cc_final: 0.8773 (mmmt) REVERT: A 50 ASN cc_start: 0.7685 (t0) cc_final: 0.7366 (t0) REVERT: A 220 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8331 (mtpt) REVERT: A 349 MET cc_start: 0.8147 (ptt) cc_final: 0.7877 (ptp) REVERT: A 353 ARG cc_start: 0.8372 (tpp-160) cc_final: 0.7987 (tpp-160) REVERT: A 374 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.6567 (t0) REVERT: B 43 MET cc_start: 0.7274 (mmm) cc_final: 0.6613 (mmm) REVERT: B 193 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6507 (ptp90) REVERT: B 223 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7271 (mm-40) REVERT: B 267 ASP cc_start: 0.8591 (t0) cc_final: 0.8328 (t0) REVERT: B 436 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7924 (ttmm) REVERT: B 446 ARG cc_start: 0.8578 (mtp85) cc_final: 0.7983 (mtp85) REVERT: C 35 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: C 81 MET cc_start: 0.8694 (mtm) cc_final: 0.7953 (mpp) REVERT: C 109 GLU cc_start: 0.8920 (pt0) cc_final: 0.8452 (mt-10) REVERT: C 218 MET cc_start: 0.8297 (mtt) cc_final: 0.7616 (mtt) REVERT: C 385 SER cc_start: 0.7634 (m) cc_final: 0.7140 (t) REVERT: C 502 LYS cc_start: 0.7794 (pttm) cc_final: 0.7418 (pttm) REVERT: C 531 ASP cc_start: 0.8730 (m-30) cc_final: 0.7490 (p0) outliers start: 81 outliers final: 61 residues processed: 360 average time/residue: 0.1632 time to fit residues: 93.1460 Evaluate side-chains 358 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 290 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 506 ARG Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 544 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 111 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 160 optimal weight: 0.0970 chunk 156 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 145 ASN A 104 ASN B 268 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101994 restraints weight = 34912.953| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.04 r_work: 0.3076 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26010 Z= 0.118 Angle : 0.477 8.656 35378 Z= 0.254 Chirality : 0.047 0.160 4088 Planarity : 0.004 0.060 4514 Dihedral : 3.810 17.918 3488 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.00 % Allowed : 20.76 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3174 helix: -0.15 (0.24), residues: 506 sheet: 0.09 (0.17), residues: 920 loop : -0.04 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 353 TYR 0.017 0.001 TYR E 329 PHE 0.023 0.001 PHE B 199 TRP 0.006 0.001 TRP F 108 HIS 0.003 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (26010) covalent geometry : angle 0.47739 / 0.25 (35378) hydrogen bonds : bond 0.03003 / 1.96 ( 886) hydrogen bonds : angle 4.96722 / 3.42 ( 2604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 113 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: F 134 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7827 (tm-30) REVERT: F 198 ASP cc_start: 0.7784 (t0) cc_final: 0.7429 (t0) REVERT: F 230 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8354 (mm-30) REVERT: F 404 ARG cc_start: 0.8384 (tpp80) cc_final: 0.7930 (tpp80) REVERT: F 436 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8200 (tttt) REVERT: D 425 ASP cc_start: 0.8728 (t0) cc_final: 0.8523 (t70) REVERT: E 17 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7321 (ptpp) REVERT: E 198 ASP cc_start: 0.7516 (t0) cc_final: 0.6808 (p0) REVERT: E 204 LYS cc_start: 0.9138 (tttt) cc_final: 0.8763 (mmmt) REVERT: A 50 ASN cc_start: 0.7666 (t0) cc_final: 0.7348 (t0) REVERT: A 134 GLU cc_start: 0.8927 (mp0) cc_final: 0.8611 (tm-30) REVERT: A 220 LYS cc_start: 0.8593 (mtpt) cc_final: 0.8301 (mtpt) REVERT: A 349 MET cc_start: 0.8144 (ptt) cc_final: 0.7880 (ptp) REVERT: A 353 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.7963 (tpp-160) REVERT: B 43 MET cc_start: 0.7280 (mmm) cc_final: 0.6612 (mmm) REVERT: B 193 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6370 (ptp90) REVERT: B 223 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7184 (mm-40) REVERT: B 267 ASP cc_start: 0.8633 (t0) cc_final: 0.8406 (t0) REVERT: B 268 ASN cc_start: 0.6719 (OUTLIER) cc_final: 0.6393 (t0) REVERT: B 436 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7537 (ttmm) REVERT: B 446 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8041 (mtp85) REVERT: C 35 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: C 57 GLU cc_start: 0.8103 (tt0) cc_final: 0.7501 (tt0) REVERT: C 81 MET cc_start: 0.8716 (mtm) cc_final: 0.7999 (mpp) REVERT: C 109 GLU cc_start: 0.8978 (pt0) cc_final: 0.8497 (mt-10) REVERT: C 218 MET cc_start: 0.8224 (mtt) cc_final: 0.7798 (mtt) REVERT: C 385 SER cc_start: 0.7496 (m) cc_final: 0.7047 (t) REVERT: C 534 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7946 (ttpt) outliers start: 59 outliers final: 50 residues processed: 344 average time/residue: 0.1775 time to fit residues: 96.4943 Evaluate side-chains 353 residues out of total 2948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 296 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 436 LYS Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 395 ILE Chi-restraints excluded: chain E residue 397 VAL Chi-restraints excluded: chain E residue 454 SER Chi-restraints excluded: chain E residue 542 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 541 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 116 optimal weight: 0.3980 chunk 217 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 288 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 310 optimal weight: 0.9980 chunk 176 optimal weight: 0.0980 chunk 312 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 145 ASN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105978 restraints weight = 34094.808| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.99 r_work: 0.3131 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26010 Z= 0.092 Angle : 0.459 7.499 35378 Z= 0.244 Chirality : 0.046 0.161 4088 Planarity : 0.004 0.056 4514 Dihedral : 3.581 15.992 3488 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.80 % Allowed : 20.79 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3174 helix: 0.08 (0.25), residues: 490 sheet: 0.22 (0.17), residues: 926 loop : 0.06 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 353 TYR 0.015 0.001 TYR B 62 PHE 0.018 0.001 PHE B 199 TRP 0.005 0.001 TRP F 108 HIS 0.003 0.001 HIS C 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (26010) covalent geometry : angle 0.45858 / 0.24 (35378) hydrogen bonds : bond 0.02731 / 1.79 ( 886) hydrogen bonds : angle 4.73056 / 3.26 ( 2604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5671.93 seconds wall clock time: 98 minutes 21.41 seconds (5901.41 seconds total)