Starting phenix.real_space_refine on Thu Mar 5 01:03:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dpw_30811/03_2026/7dpw_30811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dpw_30811/03_2026/7dpw_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_30811/03_2026/7dpw_30811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dpw_30811/03_2026/7dpw_30811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dpw_30811/03_2026/7dpw_30811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dpw_30811/03_2026/7dpw_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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17812 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "C" 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: "D" 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} Time building chain proxies: 4.10, per 1000 atoms: 0.23 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: 1.40 Conformation dependent library (CDL) restraints added in 575.9 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: 3.04 Time building geometry restraints manager: 1.82 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: 0.940 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.060 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- 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 : 0.772 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: 0.8198 (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: 0.6935 time to fit residues: 301.1610 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 : 0.617 ------------------------------------------------------------------------------- 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 = 0.136592 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: 0.2996 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- 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 : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7833 (mmt90) REVERT: A 239 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: A 247 ASN cc_start: 0.7913 (t0) cc_final: 0.7611 (t160) REVERT: A 284 GLN cc_start: 0.7703 (mt0) cc_final: 0.7364 (mp10) REVERT: A 333 GLU cc_start: 0.8232 (tt0) cc_final: 0.7719 (tt0) REVERT: A 350 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: A 387 TRP cc_start: 0.7960 (t60) cc_final: 0.7566 (t-100) REVERT: A 436 MET cc_start: 0.7111 (mtp) cc_final: 0.6212 (ttp) REVERT: A 438 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: A 448 MET cc_start: 0.8402 (mtp) cc_final: 0.7924 (mtp) REVERT: A 466 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7986 (mm110) REVERT: A 475 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: A 482 TYR cc_start: 0.8277 (m-80) cc_final: 0.7946 (m-80) REVERT: A 508 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6287 (mtp85) REVERT: B 216 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7852 (mmt90) REVERT: B 219 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8034 (ptmm) REVERT: B 239 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: B 247 ASN cc_start: 0.8177 (t0) cc_final: 0.7782 (t0) REVERT: B 256 MET cc_start: 0.8715 (mtt) cc_final: 0.8411 (mtp) REVERT: B 284 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: B 376 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6098 (pmt170) REVERT: B 387 TRP cc_start: 0.7959 (t60) cc_final: 0.7571 (t-100) REVERT: B 436 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6160 (ttp) REVERT: B 438 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: B 448 MET cc_start: 0.8400 (mtp) cc_final: 0.7992 (mtp) REVERT: B 466 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7958 (mm110) REVERT: B 472 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7798 (tppt) REVERT: B 475 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: B 482 TYR cc_start: 0.8200 (m-80) cc_final: 0.7908 (m-80) REVERT: B 508 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.6106 (mtp85) REVERT: C 156 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: C 216 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7909 (mmt90) REVERT: C 239 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: C 256 MET cc_start: 0.8761 (mtt) cc_final: 0.8454 (mtp) REVERT: C 284 GLN cc_start: 0.7708 (mt0) cc_final: 0.7364 (mp10) REVERT: C 333 GLU cc_start: 0.8223 (tt0) cc_final: 0.7693 (tt0) REVERT: C 376 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6156 (pmt170) REVERT: C 387 TRP cc_start: 0.7897 (t60) cc_final: 0.7489 (t-100) REVERT: C 438 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7187 (mt-10) REVERT: C 448 MET cc_start: 0.8410 (mtp) cc_final: 0.8014 (mtp) REVERT: C 475 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: C 482 TYR cc_start: 0.8241 (m-80) cc_final: 0.7957 (m-80) REVERT: D 156 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7945 (mmm) REVERT: D 216 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7836 (mmt90) REVERT: D 239 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8259 (mp10) REVERT: D 247 ASN cc_start: 0.8044 (t0) cc_final: 0.7720 (t160) REVERT: D 256 MET cc_start: 0.8726 (mtt) cc_final: 0.8415 (mtp) REVERT: D 284 GLN cc_start: 0.7733 (mt0) cc_final: 0.7388 (mp10) REVERT: D 362 CYS cc_start: 0.8263 (m) cc_final: 0.7883 (m) REVERT: D 376 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.5955 (pmt170) REVERT: D 387 TRP cc_start: 0.7825 (t60) cc_final: 0.7333 (t-100) REVERT: D 413 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7564 (tttm) REVERT: D 436 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6185 (ttp) REVERT: D 438 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: D 448 MET cc_start: 0.8380 (mtp) cc_final: 0.7938 (mtp) REVERT: D 466 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7992 (mm110) REVERT: D 475 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8360 (mt0) REVERT: D 482 TYR cc_start: 0.8225 (m-80) cc_final: 0.7934 (m-80) REVERT: D 508 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6299 (mtp85) outliers start: 139 outliers final: 38 residues processed: 338 average time/residue: 0.7518 time to fit residues: 277.6742 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 : 0.637 ------------------------------------------------------------------------------- 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: 0.9980 chunk 154 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** B 266 ASN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.188577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139310 restraints weight = 18098.668| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.78 r_work: 0.3170 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18136 Z= 0.143 Angle : 0.682 13.624 24604 Z= 0.325 Chirality : 0.047 0.153 2760 Planarity : 0.005 0.042 3156 Dihedral : 10.725 127.278 2631 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 6.33 % Allowed : 25.21 % Favored : 68.47 % 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: -1.35 (0.17), residues: 2216 helix: 0.34 (0.17), residues: 936 sheet: 0.06 (0.26), residues: 388 loop : -2.76 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 498 TYR 0.013 0.001 TYR B 42 PHE 0.018 0.001 PHE C 167 TRP 0.011 0.001 TRP C 124 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00330 (18136) covalent geometry : angle 0.68206 (24604) hydrogen bonds : bond 0.05004 ( 684) hydrogen bonds : angle 4.77806 ( 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 328 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 205 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8128 (ttpt) REVERT: A 130 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: A 216 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8388 (mmm160) REVERT: A 218 GLU cc_start: 0.7398 (mp0) cc_final: 0.7120 (mt-10) REVERT: A 239 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: A 247 ASN cc_start: 0.7941 (t0) cc_final: 0.7630 (t160) REVERT: A 256 MET cc_start: 0.8811 (mtt) cc_final: 0.8453 (mtp) REVERT: A 284 GLN cc_start: 0.7728 (mt0) cc_final: 0.7420 (mp10) REVERT: A 333 GLU cc_start: 0.8163 (tt0) cc_final: 0.7799 (tt0) REVERT: A 376 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.5988 (pmt170) REVERT: A 387 TRP cc_start: 0.7940 (t60) cc_final: 0.7532 (t-100) REVERT: A 436 MET cc_start: 0.7112 (mtp) cc_final: 0.6299 (ttp) REVERT: A 438 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 475 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: A 482 TYR cc_start: 0.8213 (m-80) cc_final: 0.7962 (m-80) REVERT: B 100 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8092 (ttpt) REVERT: B 130 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: B 216 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8411 (mmm160) REVERT: B 219 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8098 (ptmm) REVERT: B 239 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: B 247 ASN cc_start: 0.8162 (t0) cc_final: 0.7786 (t0) REVERT: B 284 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: B 387 TRP cc_start: 0.7852 (t60) cc_final: 0.7442 (t-100) REVERT: B 436 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6249 (ttp) REVERT: B 438 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: B 448 MET cc_start: 0.8379 (mtp) cc_final: 0.8179 (mtm) REVERT: B 475 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: B 482 TYR cc_start: 0.8167 (m-80) cc_final: 0.7854 (m-80) REVERT: C 100 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8246 (ttpt) REVERT: C 130 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: C 156 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7817 (mmm) REVERT: C 216 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7727 (mmt90) REVERT: C 223 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7641 (mm) REVERT: C 239 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: C 256 MET cc_start: 0.8717 (mtt) cc_final: 0.8414 (mtp) REVERT: C 284 GLN cc_start: 0.7712 (mt0) cc_final: 0.7400 (mp10) REVERT: C 333 GLU cc_start: 0.8179 (tt0) cc_final: 0.7813 (tt0) REVERT: C 387 TRP cc_start: 0.7886 (t60) cc_final: 0.7501 (t-100) REVERT: C 436 MET cc_start: 0.7283 (mtp) cc_final: 0.6580 (ttp) REVERT: C 438 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: C 475 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: C 482 TYR cc_start: 0.8181 (m-80) cc_final: 0.7905 (m-80) REVERT: D 100 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8092 (ttpt) REVERT: D 130 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: D 156 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7806 (mmm) REVERT: D 216 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8394 (mmm160) REVERT: D 223 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7676 (mm) REVERT: D 239 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: D 247 ASN cc_start: 0.8022 (t0) cc_final: 0.7691 (t160) REVERT: D 256 MET cc_start: 0.8678 (mtt) cc_final: 0.8372 (mtp) REVERT: D 284 GLN cc_start: 0.7718 (mt0) cc_final: 0.7414 (mp10) REVERT: D 333 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7614 (tt0) REVERT: D 387 TRP cc_start: 0.7707 (t60) cc_final: 0.7284 (t-100) REVERT: D 413 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7561 (tttm) REVERT: D 436 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.5910 (ttp) REVERT: D 438 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: D 475 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8306 (mt0) REVERT: D 482 TYR cc_start: 0.8229 (m-80) cc_final: 0.7950 (m-80) outliers start: 123 outliers final: 40 residues processed: 308 average time/residue: 0.7302 time to fit residues: 246.3541 Evaluate side-chains 262 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 188 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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 231 ASN 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 156 MET 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 543 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 156 MET 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 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: 2.9990 chunk 189 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 174 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 206 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 517 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 = 0.4126 r_free = 0.4126 target = 0.190769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.142109 restraints weight = 18006.714| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.64 r_work: 0.3226 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18136 Z= 0.118 Angle : 0.646 13.351 24604 Z= 0.305 Chirality : 0.046 0.176 2760 Planarity : 0.005 0.044 3156 Dihedral : 9.996 126.744 2611 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.78 % Favored : 95.04 % Rotamer: Outliers : 6.43 % Allowed : 24.49 % Favored : 69.08 % 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: -0.73 (0.18), residues: 2216 helix: 0.80 (0.17), residues: 944 sheet: 0.31 (0.26), residues: 388 loop : -2.35 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 383 TYR 0.012 0.001 TYR A 42 PHE 0.017 0.001 PHE D 167 TRP 0.009 0.001 TRP D 124 HIS 0.005 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00269 (18136) covalent geometry : angle 0.64558 (24604) hydrogen bonds : bond 0.04216 ( 684) hydrogen bonds : angle 4.56231 ( 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 332 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 207 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: A 216 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8409 (mmm160) REVERT: A 239 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8238 (mp10) REVERT: A 247 ASN cc_start: 0.7929 (t0) cc_final: 0.7623 (t0) REVERT: A 256 MET cc_start: 0.8793 (mtt) cc_final: 0.8455 (mtp) REVERT: A 333 GLU cc_start: 0.8170 (tt0) cc_final: 0.7815 (tt0) REVERT: A 387 TRP cc_start: 0.7822 (t60) cc_final: 0.7411 (t-100) REVERT: A 436 MET cc_start: 0.7059 (mtp) cc_final: 0.6325 (ttp) REVERT: A 475 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: A 482 TYR cc_start: 0.8150 (m-80) cc_final: 0.7878 (m-80) REVERT: B 100 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8051 (ttpt) REVERT: B 130 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: B 216 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8431 (mmm160) REVERT: B 219 LYS cc_start: 0.8414 (ptpp) cc_final: 0.8148 (ptmm) REVERT: B 239 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: B 247 ASN cc_start: 0.8108 (t0) cc_final: 0.7727 (t0) REVERT: B 256 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8479 (mtp) REVERT: B 284 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: B 290 ARG cc_start: 0.7705 (ttm-80) cc_final: 0.7299 (tpm-80) REVERT: B 387 TRP cc_start: 0.7836 (t60) cc_final: 0.7429 (t-100) REVERT: B 438 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: B 475 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: B 482 TYR cc_start: 0.8136 (m-80) cc_final: 0.7849 (m-80) REVERT: C 100 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8169 (ttpt) REVERT: C 130 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7575 (mt0) REVERT: C 216 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8404 (mmm160) REVERT: C 223 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7650 (mm) REVERT: C 239 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: C 256 MET cc_start: 0.8682 (mtt) cc_final: 0.8398 (mtp) REVERT: C 284 GLN cc_start: 0.7702 (mt0) cc_final: 0.7447 (mp10) REVERT: C 333 GLU cc_start: 0.8187 (tt0) cc_final: 0.7899 (tt0) REVERT: C 362 CYS cc_start: 0.8228 (m) cc_final: 0.7908 (m) REVERT: C 387 TRP cc_start: 0.7913 (t60) cc_final: 0.7432 (t-100) REVERT: C 475 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8223 (mt0) REVERT: C 482 TYR cc_start: 0.8143 (m-80) cc_final: 0.7935 (m-80) REVERT: D 100 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8048 (ttpt) REVERT: D 156 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7785 (mmm) REVERT: D 216 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8457 (mmm160) REVERT: D 239 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: D 247 ASN cc_start: 0.7992 (t0) cc_final: 0.7664 (t160) REVERT: D 256 MET cc_start: 0.8652 (mtt) cc_final: 0.8374 (mtp) REVERT: D 284 GLN cc_start: 0.7694 (mt0) cc_final: 0.7440 (mp10) REVERT: D 333 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7816 (tt0) REVERT: D 362 CYS cc_start: 0.8198 (m) cc_final: 0.7866 (m) REVERT: D 387 TRP cc_start: 0.7713 (t60) cc_final: 0.7209 (t-100) REVERT: D 436 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6517 (ttp) REVERT: D 475 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8237 (mt0) outliers start: 125 outliers final: 30 residues processed: 308 average time/residue: 0.7537 time to fit residues: 253.7765 Evaluate side-chains 249 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 166 GLN Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 239 GLN 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 B residue 100 LYS 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 216 ARG Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 256 MET 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 543 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 223 LEU 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 543 LEU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 413 LYS 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: 3.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 140 GLN ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.139078 restraints weight = 17936.060| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.80 r_work: 0.3167 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1870 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= 0.183 Angle : 0.707 12.631 24604 Z= 0.340 Chirality : 0.048 0.155 2760 Planarity : 0.005 0.050 3156 Dihedral : 10.104 129.390 2590 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 5.86 % Allowed : 25.87 % 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: -0.71 (0.17), residues: 2216 helix: 0.70 (0.17), residues: 940 sheet: 0.80 (0.27), residues: 348 loop : -2.30 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 498 TYR 0.014 0.001 TYR B 42 PHE 0.022 0.002 PHE D 167 TRP 0.012 0.002 TRP A 124 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00439 (18136) covalent geometry : angle 0.70739 (24604) hydrogen bonds : bond 0.05643 ( 684) hydrogen bonds : angle 4.73783 ( 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 326 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 212 time to evaluate : 0.688 Fit side-chains REVERT: A 100 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8085 (ttpt) REVERT: A 130 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: A 216 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8376 (mmm160) REVERT: A 239 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: A 247 ASN cc_start: 0.7949 (t0) cc_final: 0.7624 (t0) REVERT: A 256 MET cc_start: 0.8827 (mtt) cc_final: 0.8468 (mtp) REVERT: A 284 GLN cc_start: 0.7732 (mt0) cc_final: 0.7493 (mp10) REVERT: A 333 GLU cc_start: 0.8151 (tt0) cc_final: 0.7796 (tt0) REVERT: A 376 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.5729 (pmt170) REVERT: A 387 TRP cc_start: 0.7964 (t60) cc_final: 0.7541 (t-100) REVERT: A 475 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: A 482 TYR cc_start: 0.8239 (m-80) cc_final: 0.7943 (m-80) REVERT: B 130 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: B 216 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8371 (mmm160) REVERT: B 218 GLU cc_start: 0.7485 (mp0) cc_final: 0.7178 (mt-10) REVERT: B 219 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8104 (ptmm) REVERT: B 247 ASN cc_start: 0.8159 (t0) cc_final: 0.7764 (t0) REVERT: B 256 MET cc_start: 0.8850 (mtt) cc_final: 0.8488 (mtp) REVERT: B 284 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7389 (mp10) REVERT: B 387 TRP cc_start: 0.7869 (t60) cc_final: 0.7449 (t-100) REVERT: B 436 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6229 (ttp) REVERT: B 475 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8299 (mt0) REVERT: B 482 TYR cc_start: 0.8212 (m-80) cc_final: 0.7929 (m-80) REVERT: C 100 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8133 (ttpt) REVERT: C 130 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: C 216 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8390 (mmm160) REVERT: C 256 MET cc_start: 0.8763 (mtt) cc_final: 0.8481 (mtp) REVERT: C 284 GLN cc_start: 0.7728 (mt0) cc_final: 0.7480 (mp10) REVERT: C 333 GLU cc_start: 0.8191 (tt0) cc_final: 0.7897 (tt0) REVERT: C 387 TRP cc_start: 0.7911 (t60) cc_final: 0.7488 (t-100) REVERT: C 475 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: C 482 TYR cc_start: 0.8208 (m-80) cc_final: 0.7917 (m-80) REVERT: D 130 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: D 156 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8089 (mmm) REVERT: D 216 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8375 (mmm160) REVERT: D 239 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: D 247 ASN cc_start: 0.8030 (t0) cc_final: 0.7688 (t160) REVERT: D 256 MET cc_start: 0.8715 (mtt) cc_final: 0.8415 (mtp) REVERT: D 284 GLN cc_start: 0.7690 (mt0) cc_final: 0.7456 (mp10) REVERT: D 333 GLU cc_start: 0.8177 (tt0) cc_final: 0.7865 (tt0) REVERT: D 387 TRP cc_start: 0.7728 (t60) cc_final: 0.7287 (t-100) REVERT: D 436 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6315 (ttp) REVERT: D 475 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8313 (mt0) outliers start: 114 outliers final: 43 residues processed: 302 average time/residue: 0.6936 time to fit residues: 230.8705 Evaluate side-chains 261 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 196 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 107 LEU 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 239 GLN Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 376 ARG 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 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 188 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 284 GLN 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 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 166 GLN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG 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 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 156 MET 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 432 LEU Chi-restraints excluded: chain D residue 433 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 173 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 201 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 247 ASN ** 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 = 0.4101 r_free = 0.4101 target = 0.188322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126160 restraints weight = 17905.218| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.83 r_work: 0.3231 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18136 Z= 0.179 Angle : 0.705 12.613 24604 Z= 0.338 Chirality : 0.048 0.185 2760 Planarity : 0.005 0.047 3156 Dihedral : 10.050 128.066 2587 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.83 % Favored : 94.99 % Rotamer: Outliers : 6.28 % Allowed : 25.93 % Favored : 67.80 % 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: -0.68 (0.18), residues: 2216 helix: 0.68 (0.17), residues: 944 sheet: 0.53 (0.27), residues: 388 loop : -2.22 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 498 TYR 0.014 0.001 TYR B 42 PHE 0.019 0.002 PHE D 167 TRP 0.012 0.002 TRP A 124 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00431 (18136) covalent geometry : angle 0.70505 (24604) hydrogen bonds : bond 0.05506 ( 684) hydrogen bonds : angle 4.73986 ( 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 325 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 203 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8064 (ttpt) REVERT: A 130 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: A 216 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8290 (mmm160) REVERT: A 239 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: A 247 ASN cc_start: 0.7944 (t0) cc_final: 0.7655 (t0) REVERT: A 256 MET cc_start: 0.8790 (mtt) cc_final: 0.8404 (mtp) REVERT: A 333 GLU cc_start: 0.8074 (tt0) cc_final: 0.7742 (tt0) REVERT: A 376 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.5734 (pmt170) REVERT: A 387 TRP cc_start: 0.7964 (t60) cc_final: 0.7559 (t-100) REVERT: A 402 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6023 (tp) REVERT: A 475 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: A 482 TYR cc_start: 0.8263 (m-80) cc_final: 0.7991 (m-80) REVERT: B 100 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8058 (ttpt) REVERT: B 130 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7677 (mt0) REVERT: B 216 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8294 (mmm160) REVERT: B 219 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8109 (ptmm) REVERT: B 247 ASN cc_start: 0.8167 (t0) cc_final: 0.7802 (t0) REVERT: B 256 MET cc_start: 0.8798 (mtt) cc_final: 0.8418 (mtp) REVERT: B 387 TRP cc_start: 0.7883 (t60) cc_final: 0.7478 (t-100) REVERT: B 436 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6206 (ttp) REVERT: B 475 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: B 482 TYR cc_start: 0.8232 (m-80) cc_final: 0.7932 (m-80) REVERT: C 100 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8102 (ttpt) REVERT: C 130 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7711 (mt0) REVERT: C 216 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8338 (mmm160) REVERT: C 256 MET cc_start: 0.8723 (mtt) cc_final: 0.8448 (mtp) REVERT: C 333 GLU cc_start: 0.8091 (tt0) cc_final: 0.7761 (tt0) REVERT: C 387 TRP cc_start: 0.7936 (t60) cc_final: 0.7533 (t-100) REVERT: C 402 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6013 (tp) REVERT: C 475 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: C 482 TYR cc_start: 0.8209 (m-80) cc_final: 0.7911 (m-80) REVERT: D 100 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8095 (ttpt) REVERT: D 130 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: D 216 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8307 (mmm160) REVERT: D 239 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8105 (mp10) REVERT: D 247 ASN cc_start: 0.8020 (t0) cc_final: 0.7716 (t160) REVERT: D 256 MET cc_start: 0.8681 (mtt) cc_final: 0.8384 (mtp) REVERT: D 333 GLU cc_start: 0.8076 (tt0) cc_final: 0.7826 (tt0) REVERT: D 387 TRP cc_start: 0.7835 (t60) cc_final: 0.7398 (t-100) REVERT: D 402 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5900 (tp) REVERT: D 436 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6335 (ttp) REVERT: D 475 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8249 (mt0) outliers start: 122 outliers final: 58 residues processed: 302 average time/residue: 0.7028 time to fit residues: 233.8304 Evaluate side-chains 274 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 191 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 262 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 376 ARG 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 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 14 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 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 294 THR 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 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 14 VAL 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 294 THR Chi-restraints excluded: chain C residue 402 LEU 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 96 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 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 262 ILE Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 402 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 174 optimal weight: 0.6980 chunk 178 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 247 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.188953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129601 restraints weight = 18100.725| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.13 r_work: 0.3199 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2180 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= 0.125 Angle : 0.652 12.653 24604 Z= 0.310 Chirality : 0.046 0.212 2760 Planarity : 0.004 0.047 3156 Dihedral : 9.335 126.918 2584 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.69 % Favored : 95.13 % Rotamer: Outliers : 4.99 % Allowed : 27.16 % 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: -0.28 (0.18), residues: 2216 helix: 0.99 (0.17), residues: 952 sheet: 1.02 (0.27), residues: 348 loop : -2.03 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 498 TYR 0.013 0.001 TYR B 42 PHE 0.017 0.001 PHE D 167 TRP 0.010 0.001 TRP A 124 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00291 (18136) covalent geometry : angle 0.65209 (24604) hydrogen bonds : bond 0.04342 ( 684) hydrogen bonds : angle 4.52985 ( 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 305 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 208 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8059 (ttpt) REVERT: A 130 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: A 216 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8303 (mmm160) REVERT: A 239 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: A 247 ASN cc_start: 0.7874 (t0) cc_final: 0.7569 (t0) REVERT: A 256 MET cc_start: 0.8726 (mtt) cc_final: 0.8359 (mtp) REVERT: A 333 GLU cc_start: 0.7968 (tt0) cc_final: 0.7619 (tt0) REVERT: A 387 TRP cc_start: 0.7959 (t60) cc_final: 0.7542 (t-100) REVERT: A 475 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: A 482 TYR cc_start: 0.8265 (m-80) cc_final: 0.8018 (m-80) REVERT: B 100 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8048 (ttpt) REVERT: B 130 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: B 216 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8302 (mmm160) REVERT: B 219 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8070 (ptmm) REVERT: B 239 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: B 247 ASN cc_start: 0.8078 (t0) cc_final: 0.7715 (t0) REVERT: B 256 MET cc_start: 0.8743 (mtt) cc_final: 0.8388 (mtp) REVERT: B 290 ARG cc_start: 0.7618 (ttm-80) cc_final: 0.7215 (tpm-80) REVERT: B 362 CYS cc_start: 0.8193 (m) cc_final: 0.7870 (m) REVERT: B 387 TRP cc_start: 0.7952 (t60) cc_final: 0.7454 (t-100) REVERT: B 402 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.5853 (tp) REVERT: B 413 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7731 (tttt) REVERT: B 475 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: B 482 TYR cc_start: 0.8241 (m-80) cc_final: 0.7950 (m-80) REVERT: C 100 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8076 (ttpt) REVERT: C 130 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: C 216 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8354 (mmm160) REVERT: C 256 MET cc_start: 0.8648 (mtt) cc_final: 0.8361 (mtp) REVERT: C 333 GLU cc_start: 0.8006 (tt0) cc_final: 0.7670 (tt0) REVERT: C 387 TRP cc_start: 0.7909 (t60) cc_final: 0.7454 (t-100) REVERT: C 402 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5833 (tp) REVERT: C 456 VAL cc_start: 0.8229 (t) cc_final: 0.7988 (m) REVERT: C 475 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: C 482 TYR cc_start: 0.8219 (m-80) cc_final: 0.7936 (m-80) REVERT: D 100 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8048 (ttpt) REVERT: D 130 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: D 216 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8313 (mmm160) REVERT: D 239 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: D 247 ASN cc_start: 0.7955 (t0) cc_final: 0.7639 (t160) REVERT: D 256 MET cc_start: 0.8586 (mtt) cc_final: 0.8309 (mtp) REVERT: D 333 GLU cc_start: 0.7948 (tt0) cc_final: 0.7637 (tt0) REVERT: D 387 TRP cc_start: 0.7798 (t60) cc_final: 0.7371 (t-100) REVERT: D 475 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8221 (mt0) outliers start: 97 outliers final: 42 residues processed: 286 average time/residue: 0.6867 time to fit residues: 216.1472 Evaluate side-chains 264 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 199 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 109 LYS 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 219 LYS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 413 LYS 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 100 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 402 LEU 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 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 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 402 LEU 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 96 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 219 LYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 413 LYS 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 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 193 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** 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 = 0.4113 r_free = 0.4113 target = 0.189774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.132184 restraints weight = 18048.437| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.11 r_work: 0.3231 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18136 Z= 0.120 Angle : 0.649 12.711 24604 Z= 0.305 Chirality : 0.045 0.220 2760 Planarity : 0.004 0.054 3156 Dihedral : 9.038 125.481 2584 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.69 % Favored : 95.13 % Rotamer: Outliers : 4.48 % Allowed : 28.19 % Favored : 67.34 % 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: -0.07 (0.18), residues: 2216 helix: 1.18 (0.17), residues: 952 sheet: 0.80 (0.27), residues: 388 loop : -1.90 (0.19), residues: 876 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 A 167 TRP 0.009 0.001 TRP A 124 HIS 0.003 0.001 HIS C 365 Details of bonding type rmsd covalent geometry : bond 0.00276 (18136) covalent geometry : angle 0.64857 (24604) hydrogen bonds : bond 0.04192 ( 684) hydrogen bonds : angle 4.47723 ( 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 303 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 216 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8081 (ttpt) REVERT: A 130 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: A 216 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8290 (mmm160) REVERT: A 219 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7840 (pttm) REVERT: A 239 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8185 (mp10) REVERT: A 247 ASN cc_start: 0.7825 (t0) cc_final: 0.7550 (t0) REVERT: A 256 MET cc_start: 0.8748 (mtt) cc_final: 0.8416 (mtp) REVERT: A 333 GLU cc_start: 0.7915 (tt0) cc_final: 0.7550 (tt0) REVERT: A 341 LEU cc_start: 0.7074 (mp) cc_final: 0.6844 (mp) REVERT: A 387 TRP cc_start: 0.7945 (t60) cc_final: 0.7518 (t-100) REVERT: A 456 VAL cc_start: 0.8310 (t) cc_final: 0.8062 (m) REVERT: A 475 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8209 (mt0) REVERT: A 482 TYR cc_start: 0.8258 (m-80) cc_final: 0.7992 (m-80) REVERT: B 36 SER cc_start: 0.9191 (p) cc_final: 0.8971 (m) REVERT: B 100 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8065 (ttpt) REVERT: B 130 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: B 216 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8283 (mmm160) REVERT: B 219 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7974 (pttm) REVERT: B 247 ASN cc_start: 0.8068 (t0) cc_final: 0.7733 (t0) REVERT: B 256 MET cc_start: 0.8767 (mtt) cc_final: 0.8457 (mtp) REVERT: B 267 GLU cc_start: 0.7989 (pp20) cc_final: 0.7710 (tm-30) REVERT: B 290 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7158 (tpm-80) REVERT: B 362 CYS cc_start: 0.8179 (m) cc_final: 0.7860 (m) REVERT: B 387 TRP cc_start: 0.7960 (t60) cc_final: 0.7452 (t-100) REVERT: B 413 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7721 (tttt) REVERT: B 456 VAL cc_start: 0.8391 (t) cc_final: 0.8167 (m) REVERT: B 475 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: B 482 TYR cc_start: 0.8243 (m-80) cc_final: 0.7989 (m-80) REVERT: C 36 SER cc_start: 0.9197 (p) cc_final: 0.8972 (m) REVERT: C 100 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8143 (ttpt) REVERT: C 130 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: C 216 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8320 (mmm160) REVERT: C 256 MET cc_start: 0.8672 (mtt) cc_final: 0.8419 (mtp) REVERT: C 275 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6088 (mtt) REVERT: C 333 GLU cc_start: 0.7981 (tt0) cc_final: 0.7633 (tt0) REVERT: C 387 TRP cc_start: 0.7925 (t60) cc_final: 0.7497 (t-100) REVERT: C 413 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7226 (tttp) REVERT: C 456 VAL cc_start: 0.8235 (t) cc_final: 0.7994 (m) REVERT: C 475 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: C 482 TYR cc_start: 0.8213 (m-80) cc_final: 0.7934 (m-80) REVERT: D 36 SER cc_start: 0.9170 (p) cc_final: 0.8943 (m) REVERT: D 100 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8122 (ttpt) REVERT: D 130 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: D 216 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8254 (mmm160) REVERT: D 239 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: D 247 ASN cc_start: 0.7927 (t0) cc_final: 0.7619 (t0) REVERT: D 256 MET cc_start: 0.8609 (mtt) cc_final: 0.8323 (mtp) REVERT: D 333 GLU cc_start: 0.7936 (tt0) cc_final: 0.7661 (tt0) REVERT: D 387 TRP cc_start: 0.7798 (t60) cc_final: 0.7371 (t-100) REVERT: D 413 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7656 (tttp) REVERT: D 475 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8266 (mt0) outliers start: 87 outliers final: 42 residues processed: 288 average time/residue: 0.6718 time to fit residues: 213.9767 Evaluate side-chains 269 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 109 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 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 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 B residue 100 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 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 96 LEU Chi-restraints excluded: chain C residue 100 LYS 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 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS 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 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 D residue 96 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 219 LYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 277 LYS 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 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: 1.9990 chunk 116 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 163 optimal weight: 0.0030 chunk 68 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125178 restraints weight = 17992.398| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.88 r_work: 0.3198 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2251 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= 0.149 Angle : 0.675 12.371 24604 Z= 0.321 Chirality : 0.047 0.225 2760 Planarity : 0.005 0.061 3156 Dihedral : 9.255 127.658 2578 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.92 % Favored : 94.90 % Rotamer: Outliers : 3.96 % Allowed : 29.22 % Favored : 66.82 % 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: -0.15 (0.18), residues: 2216 helix: 1.06 (0.17), residues: 952 sheet: 0.87 (0.27), residues: 388 loop : -1.93 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 498 TYR 0.013 0.001 TYR C 42 PHE 0.020 0.002 PHE B 167 TRP 0.010 0.002 TRP A 124 HIS 0.004 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00357 (18136) covalent geometry : angle 0.67532 (24604) hydrogen bonds : bond 0.04927 ( 684) hydrogen bonds : angle 4.57233 ( 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 280 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 203 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8485 (m-30) cc_final: 0.7537 (t0) REVERT: A 100 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8114 (ttpt) REVERT: A 130 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: A 216 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8238 (mmm160) REVERT: A 219 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7872 (pttm) REVERT: A 239 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: A 247 ASN cc_start: 0.7845 (t0) cc_final: 0.7561 (t0) REVERT: A 256 MET cc_start: 0.8757 (mtt) cc_final: 0.8401 (mtp) REVERT: A 333 GLU cc_start: 0.7956 (tt0) cc_final: 0.7590 (tt0) REVERT: A 387 TRP cc_start: 0.7959 (t60) cc_final: 0.7528 (t-100) REVERT: A 475 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: A 482 TYR cc_start: 0.8265 (m-80) cc_final: 0.7978 (m-80) REVERT: B 100 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8073 (ttpt) REVERT: B 130 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: B 216 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8237 (mmm160) REVERT: B 219 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7978 (pttm) REVERT: B 239 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: B 247 ASN cc_start: 0.8087 (t0) cc_final: 0.7743 (t0) REVERT: B 256 MET cc_start: 0.8787 (mtt) cc_final: 0.8461 (mtp) REVERT: B 387 TRP cc_start: 0.7965 (t60) cc_final: 0.7536 (t-100) REVERT: B 413 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7859 (mtpt) REVERT: B 475 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: B 482 TYR cc_start: 0.8254 (m-80) cc_final: 0.7984 (m-80) REVERT: C 36 SER cc_start: 0.9171 (p) cc_final: 0.8921 (m) REVERT: C 100 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8128 (ttpt) REVERT: C 130 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: C 216 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8271 (mmm160) REVERT: C 256 MET cc_start: 0.8661 (mtt) cc_final: 0.8392 (mtp) REVERT: C 275 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6097 (mtt) REVERT: C 333 GLU cc_start: 0.8039 (tt0) cc_final: 0.7663 (tt0) REVERT: C 387 TRP cc_start: 0.7926 (t60) cc_final: 0.7489 (t-100) REVERT: C 413 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7186 (tttp) REVERT: C 456 VAL cc_start: 0.8247 (t) cc_final: 0.7998 (m) REVERT: C 475 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: C 482 TYR cc_start: 0.8222 (m-80) cc_final: 0.7948 (m-80) REVERT: D 100 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8109 (ttpt) REVERT: D 130 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: D 216 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8200 (mmm160) REVERT: D 239 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8277 (mp10) REVERT: D 247 ASN cc_start: 0.7968 (t0) cc_final: 0.7638 (t0) REVERT: D 256 MET cc_start: 0.8619 (mtt) cc_final: 0.8322 (mtp) REVERT: D 333 GLU cc_start: 0.7958 (tt0) cc_final: 0.7680 (tt0) REVERT: D 387 TRP cc_start: 0.7811 (t60) cc_final: 0.7343 (t-100) REVERT: D 413 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7673 (tttp) REVERT: D 475 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8251 (mt0) outliers start: 77 outliers final: 42 residues processed: 269 average time/residue: 0.7081 time to fit residues: 209.2324 Evaluate side-chains 269 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 109 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 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 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 B residue 100 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 438 GLU 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 96 LEU Chi-restraints excluded: chain C residue 100 LYS 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 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS 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 96 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 219 LYS Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 277 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 34 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 203 optimal weight: 5.9990 chunk 73 optimal weight: 0.0170 chunk 178 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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** ** 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 = 0.4114 r_free = 0.4114 target = 0.189955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129845 restraints weight = 17955.903| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.16 r_work: 0.3209 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18136 Z= 0.121 Angle : 0.649 12.479 24604 Z= 0.307 Chirality : 0.045 0.225 2760 Planarity : 0.004 0.063 3156 Dihedral : 8.938 125.756 2577 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.35 % Rotamer: Outliers : 3.70 % Allowed : 29.58 % Favored : 66.72 % 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: 0.02 (0.18), residues: 2216 helix: 1.21 (0.17), residues: 952 sheet: 0.88 (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 D 498 TYR 0.012 0.001 TYR B 42 PHE 0.016 0.001 PHE D 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 0.00284 (18136) covalent geometry : angle 0.64934 (24604) hydrogen bonds : bond 0.04224 ( 684) hydrogen bonds : angle 4.47423 ( 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 284 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 0.597 Fit side-chains REVERT: A 33 ASP cc_start: 0.8555 (m-30) cc_final: 0.7542 (t0) REVERT: A 100 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8093 (ttpt) REVERT: A 130 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7576 (mt0) REVERT: A 216 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8180 (mmm160) REVERT: A 219 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7824 (pttm) REVERT: A 239 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: A 247 ASN cc_start: 0.7896 (t0) cc_final: 0.7591 (t0) REVERT: A 256 MET cc_start: 0.8755 (mtt) cc_final: 0.8400 (mtp) REVERT: A 333 GLU cc_start: 0.7931 (tt0) cc_final: 0.7548 (tt0) REVERT: A 341 LEU cc_start: 0.6884 (mp) cc_final: 0.6677 (mp) REVERT: A 387 TRP cc_start: 0.7948 (t60) cc_final: 0.7494 (t-100) REVERT: A 413 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7670 (tttt) REVERT: A 456 VAL cc_start: 0.8241 (t) cc_final: 0.7984 (m) REVERT: A 475 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: A 482 TYR cc_start: 0.8241 (m-80) cc_final: 0.7958 (m-80) REVERT: B 100 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8066 (ttpt) REVERT: B 130 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: B 216 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8161 (mmm160) REVERT: B 219 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7938 (pttm) REVERT: B 239 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: B 247 ASN cc_start: 0.8091 (t0) cc_final: 0.7739 (t0) REVERT: B 256 MET cc_start: 0.8742 (mtt) cc_final: 0.8412 (mtp) REVERT: B 267 GLU cc_start: 0.7989 (pp20) cc_final: 0.7719 (tm-30) REVERT: B 290 ARG cc_start: 0.7540 (ttm-80) cc_final: 0.7093 (tpm-80) REVERT: B 387 TRP cc_start: 0.7967 (t60) cc_final: 0.7504 (t-100) REVERT: B 413 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7919 (mtpt) REVERT: B 456 VAL cc_start: 0.8344 (t) cc_final: 0.8116 (m) REVERT: B 475 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: B 482 TYR cc_start: 0.8223 (m-80) cc_final: 0.7966 (m-80) REVERT: C 100 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8101 (ttpt) REVERT: C 130 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7621 (mt0) REVERT: C 216 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8176 (mmm160) REVERT: C 219 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7880 (pttp) REVERT: C 256 MET cc_start: 0.8636 (mtt) cc_final: 0.8358 (mtp) REVERT: C 275 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6854 (mmm) REVERT: C 333 GLU cc_start: 0.8024 (tt0) cc_final: 0.7743 (tt0) REVERT: C 387 TRP cc_start: 0.7913 (t60) cc_final: 0.7469 (t-100) REVERT: C 413 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7170 (tttp) REVERT: C 456 VAL cc_start: 0.8190 (t) cc_final: 0.7938 (m) REVERT: C 475 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: C 482 TYR cc_start: 0.8193 (m-80) cc_final: 0.7928 (m-80) REVERT: D 36 SER cc_start: 0.9155 (p) cc_final: 0.8954 (m) REVERT: D 100 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8100 (ttpt) REVERT: D 110 THR cc_start: 0.9094 (t) cc_final: 0.8773 (m) REVERT: D 130 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: D 219 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7881 (pttp) REVERT: D 239 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: D 247 ASN cc_start: 0.7960 (t0) cc_final: 0.7611 (t0) REVERT: D 256 MET cc_start: 0.8588 (mtt) cc_final: 0.8287 (mtp) REVERT: D 333 GLU cc_start: 0.7943 (tt0) cc_final: 0.7620 (tt0) REVERT: D 387 TRP cc_start: 0.7823 (t60) cc_final: 0.7385 (t-100) REVERT: D 413 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7591 (tttt) REVERT: D 456 VAL cc_start: 0.8239 (t) cc_final: 0.7983 (m) REVERT: D 475 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8264 (mt0) outliers start: 72 outliers final: 38 residues processed: 273 average time/residue: 0.6668 time to fit residues: 200.6198 Evaluate side-chains 271 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 109 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 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 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 100 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 492 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LYS 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 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS 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 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 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 277 LYS 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 196 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 0.0970 chunk 213 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.186989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123728 restraints weight = 18052.660| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.88 r_work: 0.3176 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18136 Z= 0.183 Angle : 0.710 12.334 24604 Z= 0.339 Chirality : 0.048 0.225 2760 Planarity : 0.005 0.064 3156 Dihedral : 9.473 128.520 2568 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.87 % Favored : 94.95 % Rotamer: Outliers : 3.65 % Allowed : 29.73 % Favored : 66.62 % 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: -0.21 (0.18), residues: 2216 helix: 0.97 (0.17), residues: 948 sheet: 0.88 (0.27), residues: 388 loop : -1.91 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 498 TYR 0.015 0.001 TYR A 42 PHE 0.022 0.002 PHE A 167 TRP 0.012 0.002 TRP A 124 HIS 0.005 0.001 HIS B 116 Details of bonding type rmsd covalent geometry : bond 0.00441 (18136) covalent geometry : angle 0.71009 (24604) hydrogen bonds : bond 0.05554 ( 684) hydrogen bonds : angle 4.66323 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7527.36 seconds wall clock time: 128 minutes 43.20 seconds (7723.20 seconds total)