Starting phenix.real_space_refine on Tue Nov 18 22:08:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dpw_30811/11_2025/7dpw_30811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dpw_30811/11_2025/7dpw_30811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dpw_30811/11_2025/7dpw_30811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dpw_30811/11_2025/7dpw_30811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dpw_30811/11_2025/7dpw_30811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dpw_30811/11_2025/7dpw_30811.map" } resolution = 2.65 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= 0.013 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 88 5.16 5 C 11188 2.51 5 N 3104 2.21 5 O 3400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17812 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4385 Classifications: {'peptide': 556} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Restraints were copied for chains: B, C, D Time building chain proxies: 3.62, per 1000 atoms: 0.20 Number of scatterers: 17812 At special positions: 0 Unit cell: (136.74, 96.46, 124.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 24 15.00 Mg 8 11.99 O 3400 8.00 N 3104 7.00 C 11188 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: 1.67 Conformation dependent library (CDL) restraints added in 692.7 milliseconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 45.3% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 30 removed outlier: 3.637A pdb=" N ILE A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.013A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 112 through 129 removed outlier: 7.356A pdb=" N THR A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 193 through 207 Processing helix chain 'A' and resid 222 through 234 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.584A pdb=" N TYR A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 293 removed outlier: 3.883A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.548A pdb=" N ALA A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 350 removed outlier: 4.010A pdb=" N LEU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 4.048A pdb=" N TYR A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 390 Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.670A pdb=" N GLY A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.937A pdb=" N GLN A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.818A pdb=" N TYR A 529 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 526 through 530' Processing helix chain 'A' and resid 537 through 547 Processing helix chain 'A' and resid 550 through 556 removed outlier: 3.643A pdb=" N GLN A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 30 removed outlier: 3.637A pdb=" N ILE B 19 " --> pdb=" O GLY B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 79 removed outlier: 4.013A pdb=" N GLY B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 112 through 129 removed outlier: 7.356A pdb=" N THR B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 193 through 207 Processing helix chain 'B' and resid 222 through 234 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.584A pdb=" N TYR B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.883A pdb=" N GLU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.548A pdb=" N ALA B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 removed outlier: 4.010A pdb=" N LEU B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 4.048A pdb=" N TYR B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 390 Processing helix chain 'B' and resid 400 through 415 removed outlier: 3.670A pdb=" N GLY B 415 " --> pdb=" O ARG B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.937A pdb=" N GLN B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 526 through 530 removed outlier: 3.818A pdb=" N TYR B 529 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 530 " --> pdb=" O PRO B 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 530' Processing helix chain 'B' and resid 537 through 547 Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.643A pdb=" N GLN B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 30 removed outlier: 3.637A pdb=" N ILE C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.013A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 112 through 129 removed outlier: 7.356A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 169 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 193 through 207 Processing helix chain 'C' and resid 222 through 234 Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.584A pdb=" N TYR C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 293 removed outlier: 3.883A pdb=" N GLU C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 329 removed outlier: 3.548A pdb=" N ALA C 327 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 removed outlier: 4.010A pdb=" N LEU C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 4.048A pdb=" N TYR C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 400 through 415 removed outlier: 3.670A pdb=" N GLY C 415 " --> pdb=" O ARG C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.937A pdb=" N GLN C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.818A pdb=" N TYR C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 530 " --> pdb=" O PRO C 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 526 through 530' Processing helix chain 'C' and resid 537 through 547 Processing helix chain 'C' and resid 550 through 556 removed outlier: 3.643A pdb=" N GLN C 556 " --> pdb=" O ASN C 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 30 removed outlier: 3.637A pdb=" N ILE D 19 " --> pdb=" O GLY D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 79 removed outlier: 4.013A pdb=" N GLY D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 112 through 129 removed outlier: 7.356A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 251 through 259 Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.584A pdb=" N TYR D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 293 removed outlier: 3.883A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 329 removed outlier: 3.548A pdb=" N ALA D 327 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 350 removed outlier: 4.010A pdb=" N LEU D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 removed outlier: 4.048A pdb=" N TYR D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 390 Processing helix chain 'D' and resid 400 through 415 removed outlier: 3.670A pdb=" N GLY D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.937A pdb=" N GLN D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 526 through 530 removed outlier: 3.818A pdb=" N TYR D 529 " --> pdb=" O HIS D 526 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 530 " --> pdb=" O PRO D 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 526 through 530' Processing helix chain 'D' and resid 537 through 547 Processing helix chain 'D' and resid 550 through 556 removed outlier: 3.643A pdb=" N GLN D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.847A pdb=" N THR A 35 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU A 145 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 37 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS A 2 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 144 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 4 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 146 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 6 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR A 3 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA A 177 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 5 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 179 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 7 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N LEU A 181 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU A 212 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 176 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A 214 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS A 178 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG A 216 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER A 180 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 213 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE A 243 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS A 215 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.546A pdb=" N TYR A 59 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 338 removed outlier: 6.173A pdb=" N VAL A 299 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL A 335 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE A 301 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE A 337 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 303 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 366 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 367 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE A 398 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A 369 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR A 523 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 397 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 511 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A 480 " --> pdb=" O ARG A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.847A pdb=" N THR B 35 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU B 145 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 37 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS B 2 " --> pdb=" O CYS B 142 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL B 144 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 4 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU B 146 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 6 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR B 3 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 177 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 5 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 179 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 7 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N LEU B 181 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU B 212 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 176 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL B 214 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS B 178 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG B 216 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER B 180 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE B 213 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 243 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS B 215 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 60 removed outlier: 3.546A pdb=" N TYR B 59 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 331 through 338 removed outlier: 6.173A pdb=" N VAL B 299 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL B 335 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 301 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE B 337 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL B 303 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 366 " --> pdb=" O CYS B 300 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 367 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE B 398 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL B 369 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 395 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR B 523 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY B 397 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE B 520 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 511 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 480 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AA9, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.847A pdb=" N THR C 35 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU C 145 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 37 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 2 " --> pdb=" O CYS C 142 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 144 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 4 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU C 146 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 6 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR C 3 " --> pdb=" O CYS C 175 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA C 177 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C 5 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 179 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR C 7 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N LEU C 181 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU C 212 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 176 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL C 214 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS C 178 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG C 216 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER C 180 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C 213 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE C 243 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS C 215 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.546A pdb=" N TYR C 59 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 331 through 338 removed outlier: 6.173A pdb=" N VAL C 299 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL C 335 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C 301 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 366 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE C 367 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE C 398 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL C 369 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR C 523 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY C 397 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE C 511 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS C 480 " --> pdb=" O ARG C 449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.847A pdb=" N THR D 35 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLU D 145 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE D 37 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS D 2 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL D 144 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE D 4 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU D 146 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 6 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR D 3 " --> pdb=" O CYS D 175 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA D 177 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU D 5 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL D 179 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 7 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N LEU D 181 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N LEU D 212 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 176 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL D 214 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS D 178 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ARG D 216 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER D 180 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 213 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE D 243 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS D 215 " --> pdb=" O ILE D 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 59 through 60 removed outlier: 3.546A pdb=" N TYR D 59 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 331 through 338 removed outlier: 6.173A pdb=" N VAL D 299 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL D 335 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 301 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE D 337 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 366 " --> pdb=" O CYS D 300 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 367 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE D 398 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL D 369 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU D 395 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N THR D 523 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY D 397 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 511 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS D 480 " --> pdb=" O ARG D 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 433 through 435 684 hydrogen bonds defined for protein. 2040 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: 3.03 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5396 1.33 - 1.45: 2684 1.45 - 1.57: 9892 1.57 - 1.69: 40 1.69 - 1.81: 124 Bond restraints: 18136 Sorted by residual: bond pdb=" CB ARG A 204 " pdb=" CG ARG A 204 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" CB ARG D 204 " pdb=" CG ARG D 204 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" CB ARG B 204 " pdb=" CG ARG B 204 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" CB ARG C 204 " pdb=" CG ARG C 204 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.32e+00 bond pdb=" C ARG D 163 " pdb=" O ARG D 163 " ideal model delta sigma weight residual 1.236 1.253 -0.016 1.15e-02 7.56e+03 2.01e+00 ... (remaining 18131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 24072 2.30 - 4.61: 448 4.61 - 6.91: 72 6.91 - 9.21: 8 9.21 - 11.51: 4 Bond angle restraints: 24604 Sorted by residual: angle pdb=" C VAL C 489 " pdb=" N HIS C 490 " pdb=" CA HIS C 490 " ideal model delta sigma weight residual 122.06 115.46 6.60 1.86e+00 2.89e-01 1.26e+01 angle pdb=" C VAL D 489 " pdb=" N HIS D 490 " pdb=" CA HIS D 490 " ideal model delta sigma weight residual 122.06 115.46 6.60 1.86e+00 2.89e-01 1.26e+01 angle pdb=" C VAL B 489 " pdb=" N HIS B 490 " pdb=" CA HIS B 490 " ideal model delta sigma weight residual 122.06 115.46 6.60 1.86e+00 2.89e-01 1.26e+01 angle pdb=" C VAL A 489 " pdb=" N HIS A 490 " pdb=" CA HIS A 490 " ideal model delta sigma weight residual 122.06 115.46 6.60 1.86e+00 2.89e-01 1.26e+01 angle pdb=" C GLN A 166 " pdb=" N PHE A 167 " pdb=" CA PHE A 167 " ideal model delta sigma weight residual 121.14 115.06 6.08 1.75e+00 3.27e-01 1.21e+01 ... (remaining 24599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 9884 24.90 - 49.80: 896 49.80 - 74.70: 148 74.70 - 99.60: 36 99.60 - 124.50: 8 Dihedral angle restraints: 10972 sinusoidal: 4588 harmonic: 6384 Sorted by residual: dihedral pdb=" O5' CTP D 603 " pdb=" O3A CTP D 603 " pdb=" PA CTP D 603 " pdb=" PB CTP D 603 " ideal model delta sinusoidal sigma weight residual 93.05 -142.45 -124.50 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" O5' CTP C 602 " pdb=" O3A CTP C 602 " pdb=" PA CTP C 602 " pdb=" PB CTP C 602 " ideal model delta sinusoidal sigma weight residual 93.05 -142.45 -124.50 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" O5' CTP A 602 " pdb=" O3A CTP A 602 " pdb=" PA CTP A 602 " pdb=" PB CTP A 602 " ideal model delta sinusoidal sigma weight residual 93.05 -142.45 -124.50 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 10969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1356 0.035 - 0.070: 876 0.070 - 0.106: 384 0.106 - 0.141: 128 0.141 - 0.176: 16 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CB VAL C 489 " pdb=" CA VAL C 489 " pdb=" CG1 VAL C 489 " pdb=" CG2 VAL C 489 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB VAL A 489 " pdb=" CA VAL A 489 " pdb=" CG1 VAL A 489 " pdb=" CG2 VAL A 489 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB VAL B 489 " pdb=" CA VAL B 489 " pdb=" CG1 VAL B 489 " pdb=" CG2 VAL B 489 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 2757 not shown) Planarity restraints: 3156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 537 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 538 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 538 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 538 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 537 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO C 538 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 538 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 538 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 537 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 538 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 538 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 538 " -0.025 5.00e-02 4.00e+02 ... (remaining 3153 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 236 2.62 - 3.19: 15220 3.19 - 3.76: 27038 3.76 - 4.33: 40643 4.33 - 4.90: 65351 Nonbonded interactions: 148488 Sorted by model distance: nonbonded pdb=" O2A CTP C 602 " pdb="MG MG C 603 " model vdw 2.044 2.170 nonbonded pdb=" O2A CTP D 603 " pdb="MG MG D 604 " model vdw 2.044 2.170 nonbonded pdb=" O2A CTP A 602 " pdb="MG MG A 603 " model vdw 2.044 2.170 nonbonded pdb=" O2A CTP B 603 " pdb="MG MG B 604 " model vdw 2.044 2.170 nonbonded pdb=" OH TYR D 74 " pdb=" OE1 GLU D 145 " model vdw 2.125 3.040 ... (remaining 148483 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 556 or resid 602 or resid 604)) selection = (chain 'B' and (resid 1 through 556 or resid 602 or resid 604)) selection = (chain 'C' and (resid 1 through 556 or resid 602 or resid 604)) selection = (chain 'D' and (resid 1 through 556 or resid 602 or resid 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.230 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: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.500 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.008 0.048 18136 Z= 0.317 Angle : 0.798 11.513 24604 Z= 0.415 Chirality : 0.053 0.176 2760 Planarity : 0.005 0.046 3156 Dihedral : 19.093 124.497 6884 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 7.41 % Allowed : 24.90 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -3.36 (0.15), residues: 2216 helix: -1.66 (0.14), residues: 924 sheet: -0.53 (0.25), residues: 388 loop : -3.62 (0.16), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 216 TYR 0.015 0.002 TYR C 42 PHE 0.020 0.002 PHE D 167 TRP 0.011 0.002 TRP C 124 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00763 (18136) covalent geometry : angle 0.79814 (24604) hydrogen bonds : bond 0.15018 ( 684) hydrogen bonds : angle 6.85595 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 276 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7979 (mt0) cc_final: 0.7595 (mt0) REVERT: A 216 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8197 (mmt180) REVERT: A 227 GLU cc_start: 0.7820 (tp30) cc_final: 0.7530 (mm-30) REVERT: A 238 ASP cc_start: 0.7791 (m-30) cc_final: 0.7576 (m-30) REVERT: A 256 MET cc_start: 0.8281 (mtt) cc_final: 0.7956 (mtp) REVERT: A 284 GLN cc_start: 0.7186 (mt0) cc_final: 0.6955 (mp10) REVERT: A 306 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6912 (tptm) REVERT: A 334 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 387 TRP cc_start: 0.7861 (t60) cc_final: 0.7547 (t-100) REVERT: A 436 MET cc_start: 0.6650 (mtp) cc_final: 0.6301 (ttp) REVERT: A 438 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: A 448 MET cc_start: 0.8215 (mtp) cc_final: 0.7816 (mtp) REVERT: B 130 GLN cc_start: 0.7982 (mt0) cc_final: 0.7598 (mt0) REVERT: B 216 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8199 (mmt180) REVERT: B 227 GLU cc_start: 0.7863 (tp30) cc_final: 0.7607 (mm-30) REVERT: B 238 ASP cc_start: 0.7786 (m-30) cc_final: 0.7577 (m-30) REVERT: B 256 MET cc_start: 0.8283 (mtt) cc_final: 0.7981 (mtp) REVERT: B 277 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5527 (pttt) REVERT: B 334 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8601 (mt) REVERT: B 387 TRP cc_start: 0.7863 (t60) cc_final: 0.7559 (t-100) REVERT: B 438 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: B 448 MET cc_start: 0.8214 (mtp) cc_final: 0.7857 (mtp) REVERT: B 482 TYR cc_start: 0.8164 (m-80) cc_final: 0.7904 (m-80) REVERT: C 130 GLN cc_start: 0.7977 (mt0) cc_final: 0.7603 (mt0) REVERT: C 156 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7095 (mmm) REVERT: C 216 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8222 (mmt180) REVERT: C 256 MET cc_start: 0.8308 (mtt) cc_final: 0.7995 (mtp) REVERT: C 277 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5541 (pttt) REVERT: C 284 GLN cc_start: 0.7171 (mt0) cc_final: 0.6952 (mp10) REVERT: C 334 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 344 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: C 362 CYS cc_start: 0.7924 (m) cc_final: 0.7601 (m) REVERT: C 387 TRP cc_start: 0.7840 (t60) cc_final: 0.7429 (t-100) REVERT: C 438 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: C 448 MET cc_start: 0.8214 (mtp) cc_final: 0.7815 (mtp) REVERT: C 482 TYR cc_start: 0.8189 (m-80) cc_final: 0.7921 (m-80) REVERT: D 156 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7041 (mmm) REVERT: D 216 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8197 (mmt180) REVERT: D 238 ASP cc_start: 0.7796 (m-30) cc_final: 0.7593 (m-30) REVERT: D 256 MET cc_start: 0.8291 (mtt) cc_final: 0.7962 (mtp) REVERT: D 284 GLN cc_start: 0.7200 (mt0) cc_final: 0.6965 (mp10) REVERT: D 306 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6889 (tptm) REVERT: D 334 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8586 (mt) REVERT: D 362 CYS cc_start: 0.7870 (m) cc_final: 0.7598 (m) REVERT: D 387 TRP cc_start: 0.7747 (t60) cc_final: 0.7349 (t-100) REVERT: D 438 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: D 448 MET cc_start: 0.8183 (mtp) cc_final: 0.7788 (mtp) REVERT: D 482 TYR cc_start: 0.8201 (m-80) cc_final: 0.7913 (m-80) outliers start: 144 outliers final: 58 residues processed: 395 average time/residue: 0.7003 time to fit residues: 304.0963 Evaluate side-chains 295 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 218 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 344 GLU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 447 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 503 ASP Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 307 TYR Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 376 ARG Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 503 ASP Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 0.6980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 86 ASN A 266 ASN A 322 GLN A 329 ASN A 365 HIS ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 86 ASN B 266 ASN B 322 GLN B 329 ASN B 365 HIS ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN C 86 ASN C 266 ASN C 322 GLN C 329 ASN C 365 HIS ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN D 86 ASN D 322 GLN D 329 ASN D 365 HIS ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.186423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136594 restraints weight = 17941.588| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.70 r_work: 0.3132 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18136 Z= 0.191 Angle : 0.723 12.751 24604 Z= 0.356 Chirality : 0.048 0.166 2760 Planarity : 0.005 0.043 3156 Dihedral : 12.153 129.256 2709 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 7.15 % Allowed : 23.66 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -2.04 (0.17), residues: 2216 helix: -0.30 (0.16), residues: 940 sheet: -0.21 (0.26), residues: 388 loop : -3.10 (0.17), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 498 TYR 0.015 0.002 TYR D 42 PHE 0.018 0.002 PHE D 167 TRP 0.013 0.002 TRP D 124 HIS 0.006 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00451 (18136) covalent geometry : angle 0.72338 (24604) hydrogen bonds : bond 0.06040 ( 684) hydrogen bonds : angle 5.11973 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 224 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7825 (mmt90) REVERT: A 239 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: A 247 ASN cc_start: 0.7911 (t0) cc_final: 0.7611 (t160) REVERT: A 284 GLN cc_start: 0.7708 (mt0) cc_final: 0.7368 (mp10) REVERT: A 333 GLU cc_start: 0.8217 (tt0) cc_final: 0.7703 (tt0) REVERT: A 350 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: A 387 TRP cc_start: 0.7960 (t60) cc_final: 0.7568 (t-100) REVERT: A 436 MET cc_start: 0.7117 (mtp) cc_final: 0.6218 (ttp) REVERT: A 438 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: A 448 MET cc_start: 0.8403 (mtp) cc_final: 0.7927 (mtp) REVERT: A 466 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7988 (mm110) REVERT: A 475 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: A 482 TYR cc_start: 0.8280 (m-80) cc_final: 0.7951 (m-80) REVERT: A 508 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.6297 (mtp85) REVERT: B 216 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7849 (mmt90) REVERT: B 219 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8049 (ptmm) REVERT: B 239 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: B 247 ASN cc_start: 0.8178 (t0) cc_final: 0.7783 (t0) REVERT: B 256 MET cc_start: 0.8719 (mtt) cc_final: 0.8415 (mtp) REVERT: B 284 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: B 376 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6100 (pmt170) REVERT: B 387 TRP cc_start: 0.7956 (t60) cc_final: 0.7569 (t-100) REVERT: B 436 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6166 (ttp) REVERT: B 438 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: B 448 MET cc_start: 0.8400 (mtp) cc_final: 0.7995 (mtp) REVERT: B 466 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7958 (mm110) REVERT: B 472 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7803 (tppt) REVERT: B 475 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8340 (mt0) REVERT: B 482 TYR cc_start: 0.8207 (m-80) cc_final: 0.7917 (m-80) REVERT: B 508 ARG cc_start: 0.6566 (OUTLIER) cc_final: 0.6113 (mtp85) REVERT: C 156 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7977 (mmm) REVERT: C 216 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7902 (mmt90) REVERT: C 239 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: C 256 MET cc_start: 0.8763 (mtt) cc_final: 0.8456 (mtp) REVERT: C 284 GLN cc_start: 0.7711 (mt0) cc_final: 0.7366 (mp10) REVERT: C 333 GLU cc_start: 0.8213 (tt0) cc_final: 0.7683 (tt0) REVERT: C 376 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6158 (pmt170) REVERT: C 387 TRP cc_start: 0.7896 (t60) cc_final: 0.7490 (t-100) REVERT: C 438 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: C 448 MET cc_start: 0.8411 (mtp) cc_final: 0.8016 (mtp) REVERT: C 475 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: C 482 TYR cc_start: 0.8244 (m-80) cc_final: 0.7962 (m-80) REVERT: D 156 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: D 216 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7832 (mmt90) REVERT: D 239 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: D 247 ASN cc_start: 0.8042 (t0) cc_final: 0.7718 (t160) REVERT: D 256 MET cc_start: 0.8728 (mtt) cc_final: 0.8418 (mtp) REVERT: D 284 GLN cc_start: 0.7735 (mt0) cc_final: 0.7388 (mp10) REVERT: D 362 CYS cc_start: 0.8262 (m) cc_final: 0.7881 (m) REVERT: D 376 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.5958 (pmt170) REVERT: D 387 TRP cc_start: 0.7824 (t60) cc_final: 0.7333 (t-100) REVERT: D 413 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7566 (tttm) REVERT: D 436 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6193 (ttp) REVERT: D 438 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: D 448 MET cc_start: 0.8381 (mtp) cc_final: 0.7941 (mtp) REVERT: D 466 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7993 (mm110) REVERT: D 475 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: D 482 TYR cc_start: 0.8230 (m-80) cc_final: 0.7941 (m-80) REVERT: D 508 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6306 (mtp85) outliers start: 139 outliers final: 38 residues processed: 338 average time/residue: 0.7374 time to fit residues: 272.6990 Evaluate side-chains 254 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 182 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 466 GLN Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 376 ARG Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 466 GLN Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 508 ARG Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 75 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.187722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.139406 restraints weight = 18095.392| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.75 r_work: 0.3171 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18136 Z= 0.164 Angle : 0.704 13.489 24604 Z= 0.336 Chirality : 0.048 0.161 2760 Planarity : 0.005 0.043 3156 Dihedral : 10.960 127.516 2631 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.60 % Favored : 95.22 % Rotamer: Outliers : 6.17 % Allowed : 25.26 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.45 (0.17), residues: 2216 helix: 0.22 (0.17), residues: 936 sheet: 0.05 (0.26), residues: 388 loop : -2.80 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 498 TYR 0.014 0.001 TYR B 42 PHE 0.019 0.002 PHE C 167 TRP 0.012 0.002 TRP B 124 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00387 (18136) covalent geometry : angle 0.70352 (24604) hydrogen bonds : bond 0.05435 ( 684) hydrogen bonds : angle 4.85365 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 203 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8177 (ttpt) REVERT: A 130 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: A 216 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8379 (mmm160) REVERT: A 218 GLU cc_start: 0.7404 (mp0) cc_final: 0.7139 (mt-10) REVERT: A 239 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: A 247 ASN cc_start: 0.7943 (t0) cc_final: 0.7624 (t160) REVERT: A 256 MET cc_start: 0.8836 (mtt) cc_final: 0.8465 (mtp) REVERT: A 284 GLN cc_start: 0.7751 (mt0) cc_final: 0.7443 (mp10) REVERT: A 333 GLU cc_start: 0.8172 (tt0) cc_final: 0.7809 (tt0) REVERT: A 376 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6012 (pmt170) REVERT: A 387 TRP cc_start: 0.7954 (t60) cc_final: 0.7557 (t-100) REVERT: A 436 MET cc_start: 0.7143 (mtp) cc_final: 0.6428 (ttp) REVERT: A 438 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: A 448 MET cc_start: 0.8400 (mtp) cc_final: 0.7980 (mtp) REVERT: A 475 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: A 482 TYR cc_start: 0.8279 (m-80) cc_final: 0.8029 (m-80) REVERT: B 100 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8130 (ttpt) REVERT: B 130 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: B 216 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8413 (mmm160) REVERT: B 219 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8102 (ptmm) REVERT: B 239 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: B 247 ASN cc_start: 0.8198 (t0) cc_final: 0.7809 (t0) REVERT: B 284 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: B 387 TRP cc_start: 0.7857 (t60) cc_final: 0.7455 (t-100) REVERT: B 436 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6336 (ttp) REVERT: B 438 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: B 448 MET cc_start: 0.8403 (mtp) cc_final: 0.7984 (mtp) REVERT: B 475 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: B 482 TYR cc_start: 0.8214 (m-80) cc_final: 0.7890 (m-80) REVERT: C 100 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8235 (ttpt) REVERT: C 130 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: C 216 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7641 (mmt90) REVERT: C 239 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: C 256 MET cc_start: 0.8751 (mtt) cc_final: 0.8448 (mtp) REVERT: C 284 GLN cc_start: 0.7720 (mt0) cc_final: 0.7420 (mp10) REVERT: C 387 TRP cc_start: 0.7905 (t60) cc_final: 0.7533 (t-100) REVERT: C 438 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: C 448 MET cc_start: 0.8393 (mtp) cc_final: 0.7966 (mtp) REVERT: C 475 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: C 482 TYR cc_start: 0.8225 (m-80) cc_final: 0.7953 (m-80) REVERT: D 100 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8126 (ttpt) REVERT: D 130 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7658 (mt0) REVERT: D 216 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8370 (mmm160) REVERT: D 223 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7737 (mm) REVERT: D 239 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: D 247 ASN cc_start: 0.8022 (t0) cc_final: 0.7697 (t160) REVERT: D 256 MET cc_start: 0.8706 (mtt) cc_final: 0.8399 (mtp) REVERT: D 284 GLN cc_start: 0.7738 (mt0) cc_final: 0.7441 (mp10) REVERT: D 333 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7784 (tt0) REVERT: D 387 TRP cc_start: 0.7827 (t60) cc_final: 0.7431 (t-100) REVERT: D 413 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7583 (tttm) REVERT: D 436 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6330 (ttp) REVERT: D 438 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7094 (mt-10) REVERT: D 448 MET cc_start: 0.8379 (mtp) cc_final: 0.7961 (mtp) REVERT: D 475 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: D 482 TYR cc_start: 0.8245 (m-80) cc_final: 0.7986 (m-80) outliers start: 120 outliers final: 42 residues processed: 304 average time/residue: 0.7408 time to fit residues: 246.0427 Evaluate side-chains 260 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 187 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 95 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 HIS ** 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 = 0.4087 r_free = 0.4087 target = 0.186781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124496 restraints weight = 17961.784| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.82 r_work: 0.3190 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18136 Z= 0.209 Angle : 0.740 12.844 24604 Z= 0.356 Chirality : 0.050 0.173 2760 Planarity : 0.005 0.047 3156 Dihedral : 10.935 129.613 2607 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.28 % Favored : 94.54 % Rotamer: Outliers : 6.89 % Allowed : 25.26 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.27 (0.17), residues: 2216 helix: 0.23 (0.17), residues: 944 sheet: 0.16 (0.27), residues: 388 loop : -2.56 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 498 TYR 0.015 0.002 TYR B 42 PHE 0.021 0.002 PHE D 167 TRP 0.013 0.002 TRP C 124 HIS 0.006 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00503 (18136) covalent geometry : angle 0.73996 (24604) hydrogen bonds : bond 0.06200 ( 684) hydrogen bonds : angle 4.90958 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 194 time to evaluate : 0.661 Fit side-chains REVERT: A 100 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8118 (ttpt) REVERT: A 130 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: A 216 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8293 (mmm160) REVERT: A 218 GLU cc_start: 0.7466 (mp0) cc_final: 0.7264 (mt-10) REVERT: A 239 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: A 247 ASN cc_start: 0.7958 (t0) cc_final: 0.7671 (t160) REVERT: A 256 MET cc_start: 0.8802 (mtt) cc_final: 0.8394 (mtp) REVERT: A 275 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6935 (mmm) REVERT: A 284 GLN cc_start: 0.7671 (mt0) cc_final: 0.7444 (mp10) REVERT: A 333 GLU cc_start: 0.8110 (tt0) cc_final: 0.7712 (tt0) REVERT: A 376 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.5871 (pmt170) REVERT: A 387 TRP cc_start: 0.7948 (t60) cc_final: 0.7571 (t-100) REVERT: A 448 MET cc_start: 0.8411 (mtp) cc_final: 0.7967 (mtp) REVERT: A 475 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: A 482 TYR cc_start: 0.8226 (m-80) cc_final: 0.7917 (m-80) REVERT: B 130 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: B 216 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8361 (mmm160) REVERT: B 219 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8171 (ptmm) REVERT: B 239 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: B 247 ASN cc_start: 0.8206 (t0) cc_final: 0.7845 (t0) REVERT: B 256 MET cc_start: 0.8800 (mtt) cc_final: 0.8408 (mtp) REVERT: B 284 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: B 387 TRP cc_start: 0.7959 (t60) cc_final: 0.7582 (t-100) REVERT: B 436 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6252 (ttp) REVERT: B 448 MET cc_start: 0.8397 (mtp) cc_final: 0.7903 (mtp) REVERT: B 475 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: B 482 TYR cc_start: 0.8177 (m-80) cc_final: 0.7874 (m-80) REVERT: C 100 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: C 130 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: C 239 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: C 256 MET cc_start: 0.8733 (mtt) cc_final: 0.8444 (mtp) REVERT: C 284 GLN cc_start: 0.7720 (mt0) cc_final: 0.7478 (mp10) REVERT: C 333 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7782 (tt0) REVERT: C 387 TRP cc_start: 0.7923 (t60) cc_final: 0.7536 (t-100) REVERT: C 448 MET cc_start: 0.8433 (mtp) cc_final: 0.7982 (mtp) REVERT: C 475 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: C 482 TYR cc_start: 0.8197 (m-80) cc_final: 0.7925 (m-80) REVERT: D 130 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: D 239 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: D 247 ASN cc_start: 0.8042 (t0) cc_final: 0.7737 (t160) REVERT: D 256 MET cc_start: 0.8692 (mtt) cc_final: 0.8383 (mtp) REVERT: D 275 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6917 (mmm) REVERT: D 284 GLN cc_start: 0.7701 (mt0) cc_final: 0.7472 (mp10) REVERT: D 333 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7693 (tt0) REVERT: D 387 TRP cc_start: 0.7812 (t60) cc_final: 0.7390 (t-100) REVERT: D 436 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6254 (ttp) REVERT: D 448 MET cc_start: 0.8375 (mtp) cc_final: 0.7920 (mtp) REVERT: D 475 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: D 482 TYR cc_start: 0.8248 (m-80) cc_final: 0.8014 (m-80) outliers start: 134 outliers final: 56 residues processed: 307 average time/residue: 0.7493 time to fit residues: 251.7453 Evaluate side-chains 266 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 187 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 201 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.140743 restraints weight = 17933.738| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.69 r_work: 0.3205 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18136 Z= 0.131 Angle : 0.667 12.872 24604 Z= 0.317 Chirality : 0.046 0.164 2760 Planarity : 0.005 0.042 3156 Dihedral : 9.890 128.131 2595 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.78 % Favored : 95.04 % Rotamer: Outliers : 5.92 % Allowed : 25.82 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.76 (0.18), residues: 2216 helix: 0.71 (0.17), residues: 944 sheet: 0.69 (0.27), residues: 348 loop : -2.36 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 498 TYR 0.013 0.001 TYR B 42 PHE 0.017 0.001 PHE A 167 TRP 0.010 0.001 TRP B 124 HIS 0.003 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00306 (18136) covalent geometry : angle 0.66699 (24604) hydrogen bonds : bond 0.04597 ( 684) hydrogen bonds : angle 4.61498 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 210 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8064 (ttpt) REVERT: A 130 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: A 216 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8351 (mmm160) REVERT: A 239 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: A 247 ASN cc_start: 0.7962 (t0) cc_final: 0.7665 (t160) REVERT: A 256 MET cc_start: 0.8813 (mtt) cc_final: 0.8450 (mtp) REVERT: A 275 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6834 (mmm) REVERT: A 284 GLN cc_start: 0.7710 (mt0) cc_final: 0.7470 (mp10) REVERT: A 333 GLU cc_start: 0.8130 (tt0) cc_final: 0.7785 (tt0) REVERT: A 376 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.5742 (pmt170) REVERT: A 387 TRP cc_start: 0.7860 (t60) cc_final: 0.7450 (t-100) REVERT: A 475 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: A 482 TYR cc_start: 0.8215 (m-80) cc_final: 0.7961 (m-80) REVERT: B 100 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8043 (ttpt) REVERT: B 130 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7626 (mt0) REVERT: B 216 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8341 (mmm160) REVERT: B 219 LYS cc_start: 0.8361 (ptpp) cc_final: 0.8064 (ptmm) REVERT: B 239 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8200 (mp10) REVERT: B 247 ASN cc_start: 0.8164 (t0) cc_final: 0.7791 (t0) REVERT: B 256 MET cc_start: 0.8826 (mtt) cc_final: 0.8482 (mtp) REVERT: B 284 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: B 290 ARG cc_start: 0.7672 (ttm-80) cc_final: 0.7282 (tpm-80) REVERT: B 387 TRP cc_start: 0.7852 (t60) cc_final: 0.7414 (t-100) REVERT: B 413 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7744 (tttt) REVERT: B 475 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8283 (mt0) REVERT: B 482 TYR cc_start: 0.8209 (m-80) cc_final: 0.7928 (m-80) REVERT: C 100 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8175 (ttpt) REVERT: C 130 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: C 216 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8358 (mmm160) REVERT: C 223 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7663 (mm) REVERT: C 239 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: C 256 MET cc_start: 0.8739 (mtt) cc_final: 0.8463 (mtp) REVERT: C 284 GLN cc_start: 0.7727 (mt0) cc_final: 0.7483 (mp10) REVERT: C 333 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7904 (tt0) REVERT: C 362 CYS cc_start: 0.8204 (m) cc_final: 0.7881 (m) REVERT: C 387 TRP cc_start: 0.7913 (t60) cc_final: 0.7404 (t-100) REVERT: C 475 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: C 482 TYR cc_start: 0.8237 (m-80) cc_final: 0.7942 (m-80) REVERT: D 100 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8057 (ttpt) REVERT: D 130 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: D 216 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8335 (mmm160) REVERT: D 223 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7698 (mm) REVERT: D 239 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: D 247 ASN cc_start: 0.8022 (t0) cc_final: 0.7699 (t160) REVERT: D 256 MET cc_start: 0.8673 (mtt) cc_final: 0.8372 (mtp) REVERT: D 275 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6751 (mmm) REVERT: D 284 GLN cc_start: 0.7707 (mt0) cc_final: 0.7472 (mp10) REVERT: D 333 GLU cc_start: 0.8141 (tt0) cc_final: 0.7849 (tt0) REVERT: D 387 TRP cc_start: 0.7805 (t60) cc_final: 0.7416 (t-100) REVERT: D 475 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: D 482 TYR cc_start: 0.8275 (m-80) cc_final: 0.8008 (m-80) outliers start: 115 outliers final: 47 residues processed: 302 average time/residue: 0.7310 time to fit residues: 242.2162 Evaluate side-chains 265 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 191 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 173 optimal weight: 0.0030 chunk 82 optimal weight: 0.0770 chunk 212 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 overall best weight: 0.6950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.191429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142572 restraints weight = 17957.897| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.74 r_work: 0.3231 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18136 Z= 0.120 Angle : 0.645 12.951 24604 Z= 0.306 Chirality : 0.045 0.169 2760 Planarity : 0.004 0.041 3156 Dihedral : 9.336 126.423 2591 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 5.61 % Allowed : 26.49 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.38 (0.18), residues: 2216 helix: 0.99 (0.17), residues: 952 sheet: 0.55 (0.26), residues: 388 loop : -2.09 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 498 TYR 0.012 0.001 TYR B 42 PHE 0.018 0.001 PHE D 167 TRP 0.009 0.001 TRP D 124 HIS 0.003 0.001 HIS D 55 Details of bonding type rmsd covalent geometry : bond 0.00277 (18136) covalent geometry : angle 0.64533 (24604) hydrogen bonds : bond 0.04224 ( 684) hydrogen bonds : angle 4.50611 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 214 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8024 (ttpt) REVERT: A 130 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: A 216 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8375 (mmm160) REVERT: A 239 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: A 247 ASN cc_start: 0.7967 (t0) cc_final: 0.7648 (t0) REVERT: A 256 MET cc_start: 0.8797 (mtt) cc_final: 0.8467 (mtp) REVERT: A 284 GLN cc_start: 0.7666 (mt0) cc_final: 0.7463 (mp10) REVERT: A 333 GLU cc_start: 0.8048 (tt0) cc_final: 0.7719 (tt0) REVERT: A 387 TRP cc_start: 0.7968 (t60) cc_final: 0.7559 (t-100) REVERT: A 456 VAL cc_start: 0.8289 (t) cc_final: 0.8035 (m) REVERT: A 475 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: A 482 TYR cc_start: 0.8229 (m-80) cc_final: 0.7966 (m-80) REVERT: B 1 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8069 (tpp) REVERT: B 100 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: B 130 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 140 GLN cc_start: 0.8910 (mt0) cc_final: 0.8632 (mt0) REVERT: B 216 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8344 (mmm160) REVERT: B 219 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8034 (ptmm) REVERT: B 239 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8245 (mp10) REVERT: B 247 ASN cc_start: 0.8145 (t0) cc_final: 0.7745 (t0) REVERT: B 256 MET cc_start: 0.8831 (mtt) cc_final: 0.8514 (mtp) REVERT: B 290 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7256 (tpm-80) REVERT: B 362 CYS cc_start: 0.8204 (m) cc_final: 0.7830 (m) REVERT: B 387 TRP cc_start: 0.7857 (t60) cc_final: 0.7362 (t-100) REVERT: B 413 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7719 (tttt) REVERT: B 475 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: B 482 TYR cc_start: 0.8207 (m-80) cc_final: 0.7916 (m-80) REVERT: C 1 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8120 (tpp) REVERT: C 100 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8097 (ttpt) REVERT: C 130 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: C 216 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8354 (mmm160) REVERT: C 239 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8219 (mp10) REVERT: C 256 MET cc_start: 0.8704 (mtt) cc_final: 0.8438 (mtp) REVERT: C 333 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7869 (tt0) REVERT: C 362 CYS cc_start: 0.8125 (m) cc_final: 0.7810 (m) REVERT: C 387 TRP cc_start: 0.7908 (t60) cc_final: 0.7405 (t-100) REVERT: C 413 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7664 (ttpt) REVERT: C 456 VAL cc_start: 0.8232 (t) cc_final: 0.7983 (m) REVERT: C 475 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: C 482 TYR cc_start: 0.8216 (m-80) cc_final: 0.7949 (m-80) REVERT: D 100 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8064 (ttpt) REVERT: D 130 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: D 216 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8342 (mmm160) REVERT: D 239 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: D 247 ASN cc_start: 0.8005 (t0) cc_final: 0.7668 (t160) REVERT: D 256 MET cc_start: 0.8664 (mtt) cc_final: 0.8366 (mtp) REVERT: D 284 GLN cc_start: 0.7647 (mt0) cc_final: 0.7443 (mp10) REVERT: D 333 GLU cc_start: 0.8082 (tt0) cc_final: 0.7812 (tt0) REVERT: D 362 CYS cc_start: 0.8152 (m) cc_final: 0.7811 (m) REVERT: D 387 TRP cc_start: 0.7824 (t60) cc_final: 0.7301 (t-100) REVERT: D 413 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7162 (tttp) REVERT: D 475 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: D 482 TYR cc_start: 0.8264 (m-80) cc_final: 0.8031 (m-80) outliers start: 109 outliers final: 38 residues processed: 303 average time/residue: 0.7404 time to fit residues: 245.5791 Evaluate side-chains 260 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 174 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124096 restraints weight = 18073.208| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.88 r_work: 0.3196 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18136 Z= 0.171 Angle : 0.691 12.554 24604 Z= 0.330 Chirality : 0.048 0.193 2760 Planarity : 0.005 0.047 3156 Dihedral : 9.733 128.516 2587 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.92 % Favored : 94.90 % Rotamer: Outliers : 5.81 % Allowed : 26.59 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.44 (0.18), residues: 2216 helix: 0.87 (0.17), residues: 948 sheet: 0.60 (0.27), residues: 388 loop : -2.07 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 498 TYR 0.013 0.001 TYR A 42 PHE 0.021 0.002 PHE C 167 TRP 0.011 0.002 TRP C 124 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00410 (18136) covalent geometry : angle 0.69058 (24604) hydrogen bonds : bond 0.05312 ( 684) hydrogen bonds : angle 4.64874 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 197 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8124 (ttpt) REVERT: A 130 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: A 216 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8299 (mmm160) REVERT: A 239 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: A 247 ASN cc_start: 0.7913 (t0) cc_final: 0.7625 (t0) REVERT: A 256 MET cc_start: 0.8771 (mtt) cc_final: 0.8394 (mtp) REVERT: A 333 GLU cc_start: 0.7993 (tt0) cc_final: 0.7665 (tt0) REVERT: A 387 TRP cc_start: 0.7951 (t60) cc_final: 0.7517 (t-100) REVERT: A 402 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.5963 (tp) REVERT: A 475 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8304 (mt0) REVERT: A 482 TYR cc_start: 0.8273 (m-80) cc_final: 0.7988 (m-80) REVERT: B 100 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8107 (ttpt) REVERT: B 130 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: B 216 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8328 (mmm160) REVERT: B 219 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8146 (ptmm) REVERT: B 247 ASN cc_start: 0.8128 (t0) cc_final: 0.7775 (t0) REVERT: B 256 MET cc_start: 0.8797 (mtt) cc_final: 0.8432 (mtp) REVERT: B 307 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: B 387 TRP cc_start: 0.7859 (t60) cc_final: 0.7434 (t-100) REVERT: B 413 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7868 (mtpt) REVERT: B 436 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6490 (ttm) REVERT: B 475 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8227 (mt0) REVERT: B 482 TYR cc_start: 0.8272 (m-80) cc_final: 0.8004 (m-80) REVERT: C 100 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: C 130 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: C 216 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8374 (mmm160) REVERT: C 239 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: C 256 MET cc_start: 0.8680 (mtt) cc_final: 0.8395 (mtp) REVERT: C 333 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7781 (tt0) REVERT: C 387 TRP cc_start: 0.7918 (t60) cc_final: 0.7484 (t-100) REVERT: C 456 VAL cc_start: 0.8293 (t) cc_final: 0.8046 (m) REVERT: C 475 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: C 482 TYR cc_start: 0.8304 (m-80) cc_final: 0.8023 (m-80) REVERT: D 130 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7679 (mt0) REVERT: D 216 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8345 (mmm160) REVERT: D 239 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: D 247 ASN cc_start: 0.7966 (t0) cc_final: 0.7656 (t160) REVERT: D 256 MET cc_start: 0.8621 (mtt) cc_final: 0.8330 (mtp) REVERT: D 333 GLU cc_start: 0.7989 (tt0) cc_final: 0.7720 (tt0) REVERT: D 387 TRP cc_start: 0.7819 (t60) cc_final: 0.7397 (t-100) REVERT: D 402 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.5984 (tp) REVERT: D 475 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: D 482 TYR cc_start: 0.8317 (m-80) cc_final: 0.8024 (m-80) outliers start: 113 outliers final: 47 residues processed: 293 average time/residue: 0.7116 time to fit residues: 229.8201 Evaluate side-chains 265 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 194 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 0.0980 chunk 193 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN ** D 480 HIS ** 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 = 0.4108 r_free = 0.4108 target = 0.189429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127108 restraints weight = 18027.271| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.88 r_work: 0.3226 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18136 Z= 0.123 Angle : 0.653 12.652 24604 Z= 0.308 Chirality : 0.045 0.210 2760 Planarity : 0.004 0.051 3156 Dihedral : 9.251 126.512 2587 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 5.35 % Allowed : 27.11 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.18 (0.18), residues: 2216 helix: 1.11 (0.17), residues: 948 sheet: 0.72 (0.27), residues: 388 loop : -1.95 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 498 TYR 0.012 0.001 TYR B 42 PHE 0.017 0.001 PHE D 167 TRP 0.010 0.001 TRP A 124 HIS 0.004 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.00285 (18136) covalent geometry : angle 0.65299 (24604) hydrogen bonds : bond 0.04284 ( 684) hydrogen bonds : angle 4.50348 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 209 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8107 (ttpt) REVERT: A 130 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: A 216 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8246 (mmm160) REVERT: A 239 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: A 247 ASN cc_start: 0.7880 (t0) cc_final: 0.7593 (t0) REVERT: A 256 MET cc_start: 0.8769 (mtt) cc_final: 0.8381 (mtp) REVERT: A 333 GLU cc_start: 0.7909 (tt0) cc_final: 0.7611 (tt0) REVERT: A 341 LEU cc_start: 0.7027 (mp) cc_final: 0.6801 (mp) REVERT: A 387 TRP cc_start: 0.7945 (t60) cc_final: 0.7519 (t-100) REVERT: A 456 VAL cc_start: 0.8298 (t) cc_final: 0.8043 (m) REVERT: A 475 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: A 482 TYR cc_start: 0.8247 (m-80) cc_final: 0.7984 (m-80) REVERT: B 100 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8070 (ttpt) REVERT: B 130 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: B 216 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8261 (mmm160) REVERT: B 219 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7981 (pttm) REVERT: B 247 ASN cc_start: 0.8100 (t0) cc_final: 0.7772 (t0) REVERT: B 256 MET cc_start: 0.8772 (mtt) cc_final: 0.8435 (mtp) REVERT: B 290 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7150 (tpm-80) REVERT: B 387 TRP cc_start: 0.7957 (t60) cc_final: 0.7547 (t-100) REVERT: B 413 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7731 (tttt) REVERT: B 475 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: B 482 TYR cc_start: 0.8253 (m-80) cc_final: 0.7992 (m-80) REVERT: C 100 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8102 (ttpt) REVERT: C 130 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: C 216 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8312 (mmm160) REVERT: C 239 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: C 256 MET cc_start: 0.8634 (mtt) cc_final: 0.8313 (mtp) REVERT: C 333 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7749 (tt0) REVERT: C 387 TRP cc_start: 0.7903 (t60) cc_final: 0.7478 (t-100) REVERT: C 413 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7213 (tttp) REVERT: C 456 VAL cc_start: 0.8240 (t) cc_final: 0.7994 (m) REVERT: C 475 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: C 482 TYR cc_start: 0.8267 (m-80) cc_final: 0.7991 (m-80) REVERT: D 100 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8096 (ttpt) REVERT: D 130 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: D 216 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8278 (mmm160) REVERT: D 239 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: D 247 ASN cc_start: 0.7964 (t0) cc_final: 0.7637 (t0) REVERT: D 256 MET cc_start: 0.8578 (mtt) cc_final: 0.8309 (mtp) REVERT: D 333 GLU cc_start: 0.7922 (tt0) cc_final: 0.7653 (tt0) REVERT: D 362 CYS cc_start: 0.7984 (m) cc_final: 0.7680 (m) REVERT: D 387 TRP cc_start: 0.7801 (t60) cc_final: 0.7301 (t-100) REVERT: D 413 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7688 (tttp) REVERT: D 436 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6384 (ttp) REVERT: D 475 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: D 482 TYR cc_start: 0.8287 (m-80) cc_final: 0.8060 (m-80) outliers start: 104 outliers final: 47 residues processed: 295 average time/residue: 0.6907 time to fit residues: 224.6983 Evaluate side-chains 274 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 214 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** 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 = 0.4089 r_free = 0.4089 target = 0.187491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.124505 restraints weight = 17997.868| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.89 r_work: 0.3200 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18136 Z= 0.164 Angle : 0.694 12.420 24604 Z= 0.331 Chirality : 0.047 0.208 2760 Planarity : 0.005 0.060 3156 Dihedral : 9.585 127.972 2585 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.92 % Favored : 94.90 % Rotamer: Outliers : 4.06 % Allowed : 28.65 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.26 (0.18), residues: 2216 helix: 0.97 (0.17), residues: 948 sheet: 0.78 (0.27), residues: 388 loop : -1.96 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 498 TYR 0.014 0.001 TYR A 42 PHE 0.020 0.002 PHE C 167 TRP 0.011 0.002 TRP C 124 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00392 (18136) covalent geometry : angle 0.69403 (24604) hydrogen bonds : bond 0.05189 ( 684) hydrogen bonds : angle 4.62258 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 202 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8135 (ttpt) REVERT: A 130 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: A 216 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8209 (mmm160) REVERT: A 219 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7883 (pttm) REVERT: A 239 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: A 247 ASN cc_start: 0.7890 (t0) cc_final: 0.7606 (t0) REVERT: A 256 MET cc_start: 0.8788 (mtt) cc_final: 0.8410 (mtp) REVERT: A 333 GLU cc_start: 0.7951 (tt0) cc_final: 0.7638 (tt0) REVERT: A 341 LEU cc_start: 0.6989 (mp) cc_final: 0.6764 (mp) REVERT: A 387 TRP cc_start: 0.7949 (t60) cc_final: 0.7521 (t-100) REVERT: A 475 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: A 482 TYR cc_start: 0.8262 (m-80) cc_final: 0.7975 (m-80) REVERT: B 100 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8111 (ttpt) REVERT: B 130 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: B 216 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8230 (mmm160) REVERT: B 219 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8024 (pttm) REVERT: B 239 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: B 247 ASN cc_start: 0.8127 (t0) cc_final: 0.7784 (t0) REVERT: B 256 MET cc_start: 0.8808 (mtt) cc_final: 0.8449 (mtp) REVERT: B 387 TRP cc_start: 0.7973 (t60) cc_final: 0.7558 (t-100) REVERT: B 413 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7832 (mtpt) REVERT: B 475 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: B 482 TYR cc_start: 0.8261 (m-80) cc_final: 0.7987 (m-80) REVERT: C 100 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8150 (ttpt) REVERT: C 130 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: C 216 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8272 (mmm160) REVERT: C 239 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: C 256 MET cc_start: 0.8671 (mtt) cc_final: 0.8392 (mtp) REVERT: C 275 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6231 (mtt) REVERT: C 333 GLU cc_start: 0.7989 (tt0) cc_final: 0.7677 (tt0) REVERT: C 387 TRP cc_start: 0.7911 (t60) cc_final: 0.7468 (t-100) REVERT: C 456 VAL cc_start: 0.8237 (t) cc_final: 0.7983 (m) REVERT: C 475 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: C 482 TYR cc_start: 0.8288 (m-80) cc_final: 0.8001 (m-80) REVERT: D 100 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8129 (ttpt) REVERT: D 130 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: D 216 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8222 (mmm160) REVERT: D 239 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: D 247 ASN cc_start: 0.7981 (t0) cc_final: 0.7645 (t0) REVERT: D 256 MET cc_start: 0.8629 (mtt) cc_final: 0.8345 (mtp) REVERT: D 333 GLU cc_start: 0.7963 (tt0) cc_final: 0.7667 (tt0) REVERT: D 387 TRP cc_start: 0.7817 (t60) cc_final: 0.7373 (t-100) REVERT: D 413 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7679 (tttp) REVERT: D 475 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: D 482 TYR cc_start: 0.8300 (m-80) cc_final: 0.8013 (m-80) outliers start: 79 outliers final: 46 residues processed: 268 average time/residue: 0.6964 time to fit residues: 206.0349 Evaluate side-chains 268 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 197 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 LYS Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 34 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 203 optimal weight: 4.9990 chunk 73 optimal weight: 0.0020 chunk 178 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130758 restraints weight = 18006.447| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.08 r_work: 0.3240 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18136 Z= 0.119 Angle : 0.648 12.502 24604 Z= 0.307 Chirality : 0.045 0.223 2760 Planarity : 0.004 0.062 3156 Dihedral : 8.978 125.293 2584 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.29 % Favored : 95.53 % Rotamer: Outliers : 3.40 % Allowed : 29.63 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.18), residues: 2216 helix: 1.19 (0.17), residues: 952 sheet: 0.84 (0.27), residues: 388 loop : -1.81 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 498 TYR 0.011 0.001 TYR B 42 PHE 0.014 0.001 PHE C 167 TRP 0.010 0.001 TRP A 124 HIS 0.003 0.001 HIS D 116 Details of bonding type rmsd covalent geometry : bond 0.00278 (18136) covalent geometry : angle 0.64760 (24604) hydrogen bonds : bond 0.04061 ( 684) hydrogen bonds : angle 4.46073 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 0.703 Fit side-chains REVERT: A 100 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8101 (ttpt) REVERT: A 130 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: A 216 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7736 (mmm160) REVERT: A 219 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7808 (pttm) REVERT: A 239 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: A 247 ASN cc_start: 0.7854 (t0) cc_final: 0.7584 (t0) REVERT: A 256 MET cc_start: 0.8731 (mtt) cc_final: 0.8387 (mtp) REVERT: A 333 GLU cc_start: 0.7890 (tt0) cc_final: 0.7523 (tt0) REVERT: A 341 LEU cc_start: 0.7076 (mp) cc_final: 0.6875 (mp) REVERT: A 387 TRP cc_start: 0.7946 (t60) cc_final: 0.7531 (t-100) REVERT: A 413 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7690 (tttt) REVERT: A 456 VAL cc_start: 0.8240 (t) cc_final: 0.7990 (m) REVERT: A 475 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: A 482 TYR cc_start: 0.8235 (m-80) cc_final: 0.7971 (m-80) REVERT: B 36 SER cc_start: 0.9204 (p) cc_final: 0.8974 (m) REVERT: B 100 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: B 109 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: B 110 THR cc_start: 0.8986 (t) cc_final: 0.8627 (m) REVERT: B 130 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 216 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8151 (mmm160) REVERT: B 219 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7949 (pttm) REVERT: B 239 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: B 247 ASN cc_start: 0.8098 (t0) cc_final: 0.7755 (t0) REVERT: B 256 MET cc_start: 0.8720 (mtt) cc_final: 0.8401 (mtp) REVERT: B 267 GLU cc_start: 0.7929 (pp20) cc_final: 0.7668 (tm-30) REVERT: B 290 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7097 (tpm-80) REVERT: B 387 TRP cc_start: 0.7964 (t60) cc_final: 0.7515 (t-100) REVERT: B 413 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7930 (mtpt) REVERT: B 456 VAL cc_start: 0.8285 (t) cc_final: 0.8041 (m) REVERT: B 475 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: B 482 TYR cc_start: 0.8232 (m-80) cc_final: 0.7981 (m-80) REVERT: C 36 SER cc_start: 0.9189 (p) cc_final: 0.8964 (m) REVERT: C 100 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8128 (ttpt) REVERT: C 130 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7599 (mt0) REVERT: C 216 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8186 (mmm160) REVERT: C 219 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7858 (pttp) REVERT: C 239 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: C 256 MET cc_start: 0.8616 (mtt) cc_final: 0.8342 (mtp) REVERT: C 267 GLU cc_start: 0.7924 (pp20) cc_final: 0.7659 (tm-30) REVERT: C 275 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.5668 (mtt) REVERT: C 333 GLU cc_start: 0.7948 (tt0) cc_final: 0.7685 (tt0) REVERT: C 387 TRP cc_start: 0.7920 (t60) cc_final: 0.7482 (t-100) REVERT: C 413 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7235 (tttp) REVERT: C 456 VAL cc_start: 0.8177 (t) cc_final: 0.7927 (m) REVERT: C 475 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: C 482 TYR cc_start: 0.8253 (m-80) cc_final: 0.7979 (m-80) REVERT: D 36 SER cc_start: 0.9174 (p) cc_final: 0.8938 (m) REVERT: D 100 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8058 (ttpt) REVERT: D 110 THR cc_start: 0.9083 (t) cc_final: 0.8751 (m) REVERT: D 130 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: D 219 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7863 (pttp) REVERT: D 239 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: D 247 ASN cc_start: 0.7961 (t0) cc_final: 0.7633 (t0) REVERT: D 256 MET cc_start: 0.8578 (mtt) cc_final: 0.8277 (mtp) REVERT: D 333 GLU cc_start: 0.7936 (tt0) cc_final: 0.7622 (tt0) REVERT: D 387 TRP cc_start: 0.7793 (t60) cc_final: 0.7375 (t-100) REVERT: D 413 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7637 (tttt) REVERT: D 456 VAL cc_start: 0.8231 (t) cc_final: 0.7978 (m) REVERT: D 475 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: D 482 TYR cc_start: 0.8267 (m-80) cc_final: 0.8007 (m-80) outliers start: 66 outliers final: 32 residues processed: 270 average time/residue: 0.7136 time to fit residues: 212.2009 Evaluate side-chains 267 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 196 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.185485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122039 restraints weight = 18049.045| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.88 r_work: 0.3166 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 18136 Z= 0.233 Angle : 0.758 12.326 24604 Z= 0.365 Chirality : 0.051 0.219 2760 Planarity : 0.005 0.064 3156 Dihedral : 9.896 129.643 2564 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.72 % Rotamer: Outliers : 3.50 % Allowed : 29.58 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.44 (0.18), residues: 2216 helix: 0.70 (0.17), residues: 956 sheet: 0.75 (0.27), residues: 388 loop : -1.95 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 498 TYR 0.016 0.002 TYR C 264 PHE 0.021 0.002 PHE C 167 TRP 0.013 0.002 TRP A 124 HIS 0.006 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00567 (18136) covalent geometry : angle 0.75750 (24604) hydrogen bonds : bond 0.06347 ( 684) hydrogen bonds : angle 4.80820 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7728.73 seconds wall clock time: 132 minutes 6.97 seconds (7926.97 seconds total)