Starting phenix.real_space_refine on Sun Jun 15 22:48:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dpw_30811/06_2025/7dpw_30811.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dpw_30811/06_2025/7dpw_30811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dpw_30811/06_2025/7dpw_30811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dpw_30811/06_2025/7dpw_30811.map" model { file = "/net/cci-nas-00/data/ceres_data/7dpw_30811/06_2025/7dpw_30811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dpw_30811/06_2025/7dpw_30811.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17812 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4385 Classifications: {'peptide': 556} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 527} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Restraints were copied for chains: B, C, D Time building chain proxies: 10.50, per 1000 atoms: 0.59 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: 4.34 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.44 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: 7.10 Time building geometry restraints manager: 5.04 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: 0.09 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 556 or resid 602 or resid 604)) selection = (chain 'B' and (resid 1 through 556 or resid 602 or resid 604)) selection = (chain 'C' and (resid 1 through 556 or resid 602 or resid 604)) selection = (chain 'D' and (resid 1 through 556 or resid 602 or resid 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.160 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.790 ------------------------------------------------------------------------------- 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 : 9.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP C 124 HIS 0.005 0.001 HIS C 116 PHE 0.020 0.002 PHE D 167 TYR 0.015 0.002 TYR C 42 ARG 0.003 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.15018 ( 684) hydrogen bonds : angle 6.85595 ( 2040) covalent geometry : bond 0.00763 (18136) covalent geometry : angle 0.79814 (24604) *********************** 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 : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.7979 (mt0) cc_final: 0.7595 (mt0) REVERT: A 216 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8197 (mmt180) REVERT: A 227 GLU cc_start: 0.7820 (tp30) cc_final: 0.7530 (mm-30) REVERT: A 238 ASP cc_start: 0.7791 (m-30) cc_final: 0.7576 (m-30) REVERT: A 256 MET cc_start: 0.8281 (mtt) cc_final: 0.7956 (mtp) REVERT: A 284 GLN cc_start: 0.7186 (mt0) cc_final: 0.6955 (mp10) REVERT: A 306 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6912 (tptm) REVERT: A 334 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 387 TRP cc_start: 0.7861 (t60) cc_final: 0.7547 (t-100) REVERT: A 436 MET cc_start: 0.6650 (mtp) cc_final: 0.6301 (ttp) REVERT: A 438 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: A 448 MET cc_start: 0.8215 (mtp) cc_final: 0.7816 (mtp) REVERT: B 130 GLN cc_start: 0.7982 (mt0) cc_final: 0.7598 (mt0) REVERT: B 216 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8199 (mmt180) REVERT: B 227 GLU cc_start: 0.7863 (tp30) cc_final: 0.7607 (mm-30) REVERT: B 238 ASP cc_start: 0.7786 (m-30) cc_final: 0.7577 (m-30) REVERT: B 256 MET cc_start: 0.8283 (mtt) cc_final: 0.7981 (mtp) REVERT: B 277 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5527 (pttt) REVERT: B 334 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8601 (mt) REVERT: B 387 TRP cc_start: 0.7863 (t60) cc_final: 0.7559 (t-100) REVERT: B 438 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: B 448 MET cc_start: 0.8214 (mtp) cc_final: 0.7857 (mtp) REVERT: B 482 TYR cc_start: 0.8164 (m-80) cc_final: 0.7904 (m-80) REVERT: C 130 GLN cc_start: 0.7977 (mt0) cc_final: 0.7603 (mt0) REVERT: C 156 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7095 (mmm) REVERT: C 216 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8222 (mmt180) REVERT: C 256 MET cc_start: 0.8308 (mtt) cc_final: 0.7995 (mtp) REVERT: C 277 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5541 (pttt) REVERT: C 284 GLN cc_start: 0.7171 (mt0) cc_final: 0.6952 (mp10) REVERT: C 334 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 344 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: C 362 CYS cc_start: 0.7924 (m) cc_final: 0.7601 (m) REVERT: C 387 TRP cc_start: 0.7840 (t60) cc_final: 0.7429 (t-100) REVERT: C 438 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: C 448 MET cc_start: 0.8214 (mtp) cc_final: 0.7815 (mtp) REVERT: C 482 TYR cc_start: 0.8189 (m-80) cc_final: 0.7921 (m-80) REVERT: D 156 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7041 (mmm) REVERT: D 216 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8197 (mmt180) REVERT: D 238 ASP cc_start: 0.7796 (m-30) cc_final: 0.7593 (m-30) REVERT: D 256 MET cc_start: 0.8291 (mtt) cc_final: 0.7962 (mtp) REVERT: D 284 GLN cc_start: 0.7200 (mt0) cc_final: 0.6965 (mp10) REVERT: D 306 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6889 (tptm) REVERT: D 334 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8586 (mt) REVERT: D 362 CYS cc_start: 0.7870 (m) cc_final: 0.7598 (m) REVERT: D 387 TRP cc_start: 0.7747 (t60) cc_final: 0.7349 (t-100) REVERT: D 438 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: D 448 MET cc_start: 0.8183 (mtp) cc_final: 0.7788 (mtp) REVERT: D 482 TYR cc_start: 0.8201 (m-80) cc_final: 0.7913 (m-80) outliers start: 144 outliers final: 58 residues processed: 395 average time/residue: 1.4843 time to fit residues: 647.8979 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 : 2.104 ------------------------------------------------------------------------------- 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 185 optimal weight: 0.9980 chunk 166 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 322 GLN A 329 ASN A 365 HIS ** A 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 86 ASN B 322 GLN B 329 ASN B 365 HIS ** B 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN C 86 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** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.188394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138838 restraints weight = 18016.990| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.77 r_work: 0.3168 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18136 Z= 0.137 Angle : 0.672 12.618 24604 Z= 0.330 Chirality : 0.046 0.158 2760 Planarity : 0.005 0.040 3156 Dihedral : 11.653 123.096 2709 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 6.64 % Allowed : 23.87 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.17), residues: 2216 helix: -0.05 (0.17), residues: 936 sheet: -0.20 (0.26), residues: 388 loop : -3.07 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.009 0.001 HIS B 517 PHE 0.014 0.001 PHE A 167 TYR 0.013 0.001 TYR D 42 ARG 0.007 0.001 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 684) hydrogen bonds : angle 4.95670 ( 2040) covalent geometry : bond 0.00312 (18136) covalent geometry : angle 0.67244 (24604) *********************** 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 354 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 225 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7855 (mmt180) REVERT: A 239 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: A 247 ASN cc_start: 0.7880 (t0) cc_final: 0.7575 (t160) REVERT: A 284 GLN cc_start: 0.7647 (mt0) cc_final: 0.7295 (mp10) REVERT: A 333 GLU cc_start: 0.8182 (tt0) cc_final: 0.7666 (tt0) REVERT: A 350 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: A 387 TRP cc_start: 0.7936 (t60) cc_final: 0.7557 (t-100) REVERT: A 436 MET cc_start: 0.7164 (mtp) cc_final: 0.6241 (ttp) REVERT: A 438 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: A 448 MET cc_start: 0.8363 (mtp) cc_final: 0.7932 (mtp) REVERT: A 475 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: A 482 TYR cc_start: 0.8227 (m-80) cc_final: 0.7889 (m-80) REVERT: A 497 MET cc_start: 0.7440 (tpp) cc_final: 0.7230 (ttm) REVERT: A 508 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.6205 (mtp85) REVERT: B 216 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7855 (mmt180) REVERT: B 219 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7964 (ptmm) REVERT: B 239 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: B 247 ASN cc_start: 0.8147 (t0) cc_final: 0.7814 (t160) REVERT: B 256 MET cc_start: 0.8675 (mtt) cc_final: 0.8369 (mtp) REVERT: B 284 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: B 376 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6117 (pmt170) REVERT: B 387 TRP cc_start: 0.7929 (t60) cc_final: 0.7531 (t-100) REVERT: B 436 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6007 (ttp) REVERT: B 438 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: B 472 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7797 (tppt) REVERT: B 475 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: B 482 TYR cc_start: 0.8166 (m-80) cc_final: 0.7889 (m-80) REVERT: B 508 ARG cc_start: 0.6471 (OUTLIER) cc_final: 0.5928 (mtp85) REVERT: C 156 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7786 (mmm) REVERT: C 216 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.7871 (mmt180) REVERT: C 239 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: C 256 MET cc_start: 0.8721 (mtt) cc_final: 0.8427 (mtp) REVERT: C 284 GLN cc_start: 0.7625 (mt0) cc_final: 0.7271 (mp10) REVERT: C 333 GLU cc_start: 0.8154 (tt0) cc_final: 0.7622 (tt0) REVERT: C 376 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6183 (pmt170) REVERT: C 387 TRP cc_start: 0.7876 (t60) cc_final: 0.7510 (t-100) REVERT: C 436 MET cc_start: 0.7206 (mtp) cc_final: 0.6237 (ttp) REVERT: C 438 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: C 448 MET cc_start: 0.8362 (mtp) cc_final: 0.7940 (mtp) REVERT: C 475 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: C 482 TYR cc_start: 0.8194 (m-80) cc_final: 0.7898 (m-80) REVERT: C 497 MET cc_start: 0.7470 (tpp) cc_final: 0.7253 (ttm) REVERT: C 508 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.6251 (mtp85) REVERT: D 156 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7752 (mmm) REVERT: D 216 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7886 (mmt180) REVERT: D 227 GLU cc_start: 0.8698 (tp30) cc_final: 0.8481 (mm-30) REVERT: D 239 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: D 247 ASN cc_start: 0.8015 (t0) cc_final: 0.7687 (t160) REVERT: D 256 MET cc_start: 0.8678 (mtt) cc_final: 0.8358 (mtp) REVERT: D 284 GLN cc_start: 0.7648 (mt0) cc_final: 0.7298 (mp10) REVERT: D 362 CYS cc_start: 0.8286 (m) cc_final: 0.7887 (m) REVERT: D 376 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.5958 (pmt170) REVERT: D 387 TRP cc_start: 0.7791 (t60) cc_final: 0.7293 (t-100) REVERT: D 436 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6087 (ttp) REVERT: D 438 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: D 448 MET cc_start: 0.8312 (mtp) cc_final: 0.7884 (mtp) REVERT: D 475 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: D 482 TYR cc_start: 0.8182 (m-80) cc_final: 0.7927 (m-80) REVERT: D 508 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6163 (mtp85) outliers start: 129 outliers final: 31 residues processed: 328 average time/residue: 1.5947 time to fit residues: 573.2001 Evaluate side-chains 240 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 178 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 110 THR 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 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 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU 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 508 ARG Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 156 MET 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 489 VAL Chi-restraints excluded: chain C residue 508 ARG Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 96 LEU 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 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 432 LEU 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 508 ARG Chi-restraints excluded: chain D residue 514 LEU 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 202 optimal weight: 0.0000 chunk 23 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.188047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139551 restraints weight = 17980.925| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.74 r_work: 0.3180 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18136 Z= 0.161 Angle : 0.701 13.670 24604 Z= 0.334 Chirality : 0.047 0.157 2760 Planarity : 0.005 0.041 3156 Dihedral : 10.848 128.748 2627 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.60 % Favored : 95.22 % Rotamer: Outliers : 6.43 % Allowed : 24.85 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2216 helix: 0.31 (0.17), residues: 936 sheet: 0.07 (0.26), residues: 388 loop : -2.76 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 124 HIS 0.005 0.001 HIS D 55 PHE 0.020 0.002 PHE C 167 TYR 0.014 0.001 TYR D 42 ARG 0.007 0.000 ARG A 330 Details of bonding type rmsd hydrogen bonds : bond 0.05442 ( 684) hydrogen bonds : angle 4.82042 ( 2040) covalent geometry : bond 0.00375 (18136) covalent geometry : angle 0.70083 (24604) *********************** 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 333 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 208 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8178 (ttpt) REVERT: A 216 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8395 (mmm160) REVERT: A 239 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: A 247 ASN cc_start: 0.7895 (t0) cc_final: 0.7591 (t160) REVERT: A 256 MET cc_start: 0.8828 (mtt) cc_final: 0.8471 (mtp) REVERT: A 284 GLN cc_start: 0.7738 (mt0) cc_final: 0.7430 (mp10) REVERT: A 333 GLU cc_start: 0.8168 (tt0) cc_final: 0.7803 (tt0) REVERT: A 376 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6030 (pmt170) REVERT: A 387 TRP cc_start: 0.7843 (t60) cc_final: 0.7453 (t-100) REVERT: A 436 MET cc_start: 0.7161 (mtp) cc_final: 0.6430 (ttp) REVERT: A 438 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: A 448 MET cc_start: 0.8425 (mtp) cc_final: 0.7941 (mtp) REVERT: A 475 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8314 (mt0) REVERT: A 482 TYR cc_start: 0.8260 (m-80) cc_final: 0.7916 (m-80) REVERT: B 100 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8116 (ttpt) REVERT: B 216 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8416 (mmm160) REVERT: B 219 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8097 (ptmm) REVERT: B 239 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: B 247 ASN cc_start: 0.8210 (t0) cc_final: 0.7844 (t0) REVERT: B 284 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: B 387 TRP cc_start: 0.7850 (t60) cc_final: 0.7436 (t-100) REVERT: B 436 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.5955 (ttp) REVERT: B 438 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7123 (mt-10) REVERT: B 475 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: B 482 TYR cc_start: 0.8175 (m-80) cc_final: 0.7955 (m-80) REVERT: C 100 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8254 (ttpt) REVERT: C 216 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7666 (mmt90) REVERT: C 239 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: C 256 MET cc_start: 0.8743 (mtt) cc_final: 0.8436 (mtp) REVERT: C 284 GLN cc_start: 0.7743 (mt0) cc_final: 0.7436 (mp10) REVERT: C 387 TRP cc_start: 0.7933 (t60) cc_final: 0.7544 (t-100) REVERT: C 436 MET cc_start: 0.7197 (mtp) cc_final: 0.6405 (ttp) REVERT: C 438 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7183 (mt-10) REVERT: C 448 MET cc_start: 0.8380 (mtp) cc_final: 0.7917 (mtp) REVERT: C 475 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: C 482 TYR cc_start: 0.8218 (m-80) cc_final: 0.8007 (m-80) REVERT: D 100 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8115 (ttpt) REVERT: D 156 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7865 (mmm) REVERT: D 216 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7581 (mmt90) REVERT: D 239 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: D 247 ASN cc_start: 0.8020 (t0) cc_final: 0.7695 (t160) REVERT: D 256 MET cc_start: 0.8706 (mtt) cc_final: 0.8391 (mtp) REVERT: D 284 GLN cc_start: 0.7755 (mt0) cc_final: 0.7456 (mp10) REVERT: D 333 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7637 (tt0) REVERT: D 367 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8211 (mm) REVERT: D 387 TRP cc_start: 0.7715 (t60) cc_final: 0.7322 (t-100) REVERT: D 413 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7524 (tttm) REVERT: D 436 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.5958 (ttp) REVERT: D 438 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: D 475 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: D 482 TYR cc_start: 0.8184 (m-80) cc_final: 0.7915 (m-80) outliers start: 125 outliers final: 43 residues processed: 316 average time/residue: 1.5725 time to fit residues: 545.8089 Evaluate side-chains 262 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 191 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 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 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 14 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LYS 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 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 128 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 166 GLN 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 239 GLN Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 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 142 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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** ** C 517 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 = 0.4089 r_free = 0.4089 target = 0.186969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137275 restraints weight = 17965.691| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.74 r_work: 0.3146 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18136 Z= 0.204 Angle : 0.734 12.777 24604 Z= 0.353 Chirality : 0.050 0.170 2760 Planarity : 0.005 0.042 3156 Dihedral : 10.981 129.040 2612 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.10 % Favored : 94.72 % Rotamer: Outliers : 6.64 % Allowed : 24.49 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2216 helix: 0.35 (0.17), residues: 940 sheet: 0.51 (0.27), residues: 348 loop : -2.57 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 124 HIS 0.005 0.001 HIS B 116 PHE 0.021 0.002 PHE D 167 TYR 0.015 0.002 TYR B 42 ARG 0.008 0.001 ARG C 383 Details of bonding type rmsd hydrogen bonds : bond 0.06090 ( 684) hydrogen bonds : angle 4.88896 ( 2040) covalent geometry : bond 0.00491 (18136) covalent geometry : angle 0.73368 (24604) *********************** 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 326 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 197 time to evaluate : 2.038 Fit side-chains revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8124 (ttpt) REVERT: A 130 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: A 216 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8335 (mmm160) REVERT: A 239 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8143 (mp10) REVERT: A 247 ASN cc_start: 0.7937 (t0) cc_final: 0.7615 (t160) REVERT: A 256 MET cc_start: 0.8834 (mtt) cc_final: 0.8450 (mtp) REVERT: A 275 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6883 (mmm) REVERT: A 284 GLN cc_start: 0.7729 (mt0) cc_final: 0.7470 (mp10) REVERT: A 333 GLU cc_start: 0.8167 (tt0) cc_final: 0.7802 (tt0) REVERT: A 376 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.5878 (pmt170) REVERT: A 387 TRP cc_start: 0.7957 (t60) cc_final: 0.7561 (t-100) REVERT: A 436 MET cc_start: 0.7081 (mtp) cc_final: 0.6370 (ttp) REVERT: A 438 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: A 448 MET cc_start: 0.8415 (mtp) cc_final: 0.7928 (mtp) REVERT: A 475 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: A 482 TYR cc_start: 0.8216 (m-80) cc_final: 0.7953 (m-80) REVERT: B 100 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8112 (ttpt) REVERT: B 216 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8373 (mmm160) REVERT: B 218 GLU cc_start: 0.7412 (mp0) cc_final: 0.7180 (mt-10) REVERT: B 219 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8167 (ptmm) REVERT: B 239 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: B 247 ASN cc_start: 0.8191 (t0) cc_final: 0.7812 (t0) REVERT: B 256 MET cc_start: 0.8851 (mtt) cc_final: 0.8476 (mtp) REVERT: B 284 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: B 387 TRP cc_start: 0.7978 (t60) cc_final: 0.7552 (t-100) REVERT: B 436 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6342 (ttp) REVERT: B 438 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: B 475 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: B 482 TYR cc_start: 0.8132 (m-80) cc_final: 0.7844 (m-80) REVERT: C 100 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8160 (ttpt) REVERT: C 130 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7762 (mt0) REVERT: C 239 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8148 (mp10) REVERT: C 256 MET cc_start: 0.8779 (mtt) cc_final: 0.8489 (mtp) REVERT: C 284 GLN cc_start: 0.7745 (mt0) cc_final: 0.7492 (mp10) REVERT: C 333 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7814 (tt0) REVERT: C 387 TRP cc_start: 0.7929 (t60) cc_final: 0.7518 (t-100) REVERT: C 438 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: C 448 MET cc_start: 0.8449 (mtp) cc_final: 0.7986 (mtp) REVERT: C 475 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: C 482 TYR cc_start: 0.8221 (m-80) cc_final: 0.7954 (m-80) REVERT: D 130 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: D 216 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8391 (mmm160) REVERT: D 239 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: D 247 ASN cc_start: 0.8044 (t0) cc_final: 0.7715 (t160) REVERT: D 256 MET cc_start: 0.8735 (mtt) cc_final: 0.8422 (mtp) REVERT: D 284 GLN cc_start: 0.7724 (mt0) cc_final: 0.7475 (mp10) REVERT: D 333 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7687 (tt0) REVERT: D 387 TRP cc_start: 0.7831 (t60) cc_final: 0.7418 (t-100) REVERT: D 436 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6369 (ttp) REVERT: D 438 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: D 475 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8361 (mt0) outliers start: 129 outliers final: 52 residues processed: 306 average time/residue: 1.5706 time to fit residues: 527.7685 Evaluate side-chains 267 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 188 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 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 275 MET Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 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 14 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 128 VAL 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 239 GLN Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 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 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 128 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 166 GLN Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 166 GLN 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 239 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 121 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 151 optimal weight: 0.0040 chunk 196 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 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 = 0.4127 r_free = 0.4127 target = 0.190667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141508 restraints weight = 18055.512| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.73 r_work: 0.3213 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18136 Z= 0.122 Angle : 0.657 12.813 24604 Z= 0.312 Chirality : 0.045 0.154 2760 Planarity : 0.005 0.040 3156 Dihedral : 10.047 126.947 2607 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.74 % Favored : 95.08 % Rotamer: Outliers : 5.45 % Allowed : 25.41 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2216 helix: 0.83 (0.17), residues: 948 sheet: 0.38 (0.26), residues: 388 loop : -2.29 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 124 HIS 0.003 0.001 HIS D 517 PHE 0.016 0.001 PHE D 167 TYR 0.012 0.001 TYR A 42 ARG 0.009 0.001 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 684) hydrogen bonds : angle 4.57764 ( 2040) covalent geometry : bond 0.00280 (18136) covalent geometry : angle 0.65730 (24604) *********************** 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 321 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 215 time to evaluate : 2.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8095 (ttpt) REVERT: A 216 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8358 (mmm160) REVERT: A 239 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: A 247 ASN cc_start: 0.7963 (t0) cc_final: 0.7631 (t0) REVERT: A 256 MET cc_start: 0.8758 (mtt) cc_final: 0.8411 (mtp) REVERT: A 284 GLN cc_start: 0.7683 (mt0) cc_final: 0.7433 (mp10) REVERT: A 333 GLU cc_start: 0.8103 (tt0) cc_final: 0.7744 (tt0) REVERT: A 376 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.5714 (pmt170) REVERT: A 387 TRP cc_start: 0.7835 (t60) cc_final: 0.7396 (t-100) REVERT: A 475 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: A 482 TYR cc_start: 0.8164 (m-80) cc_final: 0.7921 (m-80) REVERT: B 100 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: B 130 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: B 216 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8356 (mmm160) REVERT: B 219 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8073 (ptmm) REVERT: B 239 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: B 247 ASN cc_start: 0.8166 (t0) cc_final: 0.7785 (t0) REVERT: B 256 MET cc_start: 0.8780 (mtt) cc_final: 0.8423 (mtp) REVERT: B 284 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: B 290 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7264 (tpm-80) REVERT: B 362 CYS cc_start: 0.8217 (m) cc_final: 0.7763 (m) REVERT: B 387 TRP cc_start: 0.7858 (t60) cc_final: 0.7339 (t-100) REVERT: B 413 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7763 (tttt) REVERT: B 475 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: B 482 TYR cc_start: 0.8168 (m-80) cc_final: 0.7890 (m-80) REVERT: C 100 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8130 (ttpt) REVERT: C 216 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8355 (mmm160) REVERT: C 239 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: C 256 MET cc_start: 0.8704 (mtt) cc_final: 0.8427 (mtp) REVERT: C 284 GLN cc_start: 0.7731 (mt0) cc_final: 0.7472 (mp10) REVERT: C 333 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7808 (tt0) REVERT: C 362 CYS cc_start: 0.8244 (m) cc_final: 0.7908 (m) REVERT: C 387 TRP cc_start: 0.7892 (t60) cc_final: 0.7375 (t-100) REVERT: C 475 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: C 482 TYR cc_start: 0.8178 (m-80) cc_final: 0.7913 (m-80) REVERT: D 100 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8042 (ttpt) REVERT: D 130 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7603 (mt0) REVERT: D 216 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8365 (mmm160) REVERT: D 239 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: D 247 ASN cc_start: 0.8006 (t0) cc_final: 0.7676 (t160) REVERT: D 256 MET cc_start: 0.8642 (mtt) cc_final: 0.8305 (mtp) REVERT: D 284 GLN cc_start: 0.7693 (mt0) cc_final: 0.7446 (mp10) REVERT: D 333 GLU cc_start: 0.8075 (tt0) cc_final: 0.7799 (tt0) REVERT: D 362 CYS cc_start: 0.8197 (m) cc_final: 0.7869 (m) REVERT: D 387 TRP cc_start: 0.7819 (t60) cc_final: 0.7320 (t-100) REVERT: D 475 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8258 (mt0) outliers start: 106 outliers final: 42 residues processed: 299 average time/residue: 1.5401 time to fit residues: 505.8154 Evaluate side-chains 259 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 149 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 262 ILE Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 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 284 GLN Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 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 100 LYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 475 GLN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 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 216 ARG Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 24 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 161 optimal weight: 0.0970 chunk 201 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 137 optimal weight: 0.0870 chunk 142 optimal weight: 2.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- 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 140 GLN C 247 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.189288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127623 restraints weight = 18020.614| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.17 r_work: 0.3199 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18136 Z= 0.155 Angle : 0.683 12.729 24604 Z= 0.326 Chirality : 0.047 0.170 2760 Planarity : 0.005 0.048 3156 Dihedral : 9.771 128.599 2587 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.69 % Favored : 95.13 % Rotamer: Outliers : 5.09 % Allowed : 26.49 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2216 helix: 0.88 (0.17), residues: 944 sheet: 0.48 (0.27), residues: 388 loop : -2.19 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 124 HIS 0.004 0.001 HIS B 116 PHE 0.020 0.002 PHE D 167 TYR 0.013 0.001 TYR B 42 ARG 0.011 0.001 ARG D 498 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 684) hydrogen bonds : angle 4.65174 ( 2040) covalent geometry : bond 0.00367 (18136) covalent geometry : angle 0.68333 (24604) *********************** 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 304 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 205 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8085 (ttpt) REVERT: A 216 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8324 (mmm160) REVERT: A 239 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: A 247 ASN cc_start: 0.7960 (t0) cc_final: 0.7647 (t0) REVERT: A 256 MET cc_start: 0.8800 (mtt) cc_final: 0.8444 (mtp) REVERT: A 333 GLU cc_start: 0.8068 (tt0) cc_final: 0.7728 (tt0) REVERT: A 376 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.5671 (pmt170) REVERT: A 387 TRP cc_start: 0.7842 (t60) cc_final: 0.7417 (t-100) REVERT: A 475 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: A 482 TYR cc_start: 0.8185 (m-80) cc_final: 0.7928 (m-80) REVERT: B 100 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8087 (ttpt) REVERT: B 130 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: B 216 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8348 (mmm160) REVERT: B 219 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8086 (ptmm) REVERT: B 239 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: B 247 ASN cc_start: 0.8126 (t0) cc_final: 0.7744 (t0) REVERT: B 256 MET cc_start: 0.8829 (mtt) cc_final: 0.8477 (mtp) REVERT: B 387 TRP cc_start: 0.7857 (t60) cc_final: 0.7436 (t-100) REVERT: B 413 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7833 (ttpt) REVERT: B 475 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (mt0) REVERT: B 482 TYR cc_start: 0.8152 (m-80) cc_final: 0.7885 (m-80) REVERT: C 100 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: C 216 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8370 (mmm160) REVERT: C 239 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: C 256 MET cc_start: 0.8720 (mtt) cc_final: 0.8442 (mtp) REVERT: C 284 GLN cc_start: 0.7708 (mt0) cc_final: 0.7506 (mp10) REVERT: C 333 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7793 (tt0) REVERT: C 387 TRP cc_start: 0.7792 (t60) cc_final: 0.7338 (t-100) REVERT: C 402 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5830 (tp) REVERT: C 475 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: C 482 TYR cc_start: 0.8179 (m-80) cc_final: 0.7907 (m-80) REVERT: D 100 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8093 (ttpt) REVERT: D 130 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: D 216 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8369 (mmm160) REVERT: D 239 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: D 247 ASN cc_start: 0.8027 (t0) cc_final: 0.7693 (t160) REVERT: D 256 MET cc_start: 0.8692 (mtt) cc_final: 0.8408 (mtp) REVERT: D 284 GLN cc_start: 0.7699 (mt0) cc_final: 0.7497 (mp10) REVERT: D 333 GLU cc_start: 0.8088 (tt0) cc_final: 0.7784 (tt0) REVERT: D 387 TRP cc_start: 0.7704 (t60) cc_final: 0.7247 (t-100) REVERT: D 402 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5868 (tp) REVERT: D 475 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8302 (mt0) outliers start: 99 outliers final: 40 residues processed: 286 average time/residue: 1.5447 time to fit residues: 486.4607 Evaluate side-chains 255 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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 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 376 ARG Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 413 LYS Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 448 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 109 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 389 ARG 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 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 239 GLN Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 475 GLN Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 543 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 206 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** ** 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 = 0.4115 r_free = 0.4115 target = 0.190063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127945 restraints weight = 18034.953| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.18 r_work: 0.3238 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18136 Z= 0.115 Angle : 0.641 12.608 24604 Z= 0.303 Chirality : 0.045 0.225 2760 Planarity : 0.005 0.053 3156 Dihedral : 9.107 125.526 2587 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 4.27 % Allowed : 27.57 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2216 helix: 1.13 (0.17), residues: 952 sheet: 0.60 (0.26), residues: 388 loop : -1.97 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.003 0.001 HIS A 365 PHE 0.016 0.001 PHE D 167 TYR 0.012 0.001 TYR B 42 ARG 0.013 0.001 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 684) hydrogen bonds : angle 4.45309 ( 2040) covalent geometry : bond 0.00264 (18136) covalent geometry : angle 0.64084 (24604) *********************** 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 301 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 218 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8513 (m-30) cc_final: 0.7533 (t0) REVERT: A 100 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8083 (ttpt) REVERT: A 216 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8315 (mmm160) REVERT: A 239 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: A 247 ASN cc_start: 0.7859 (t0) cc_final: 0.7572 (t0) REVERT: A 256 MET cc_start: 0.8702 (mtt) cc_final: 0.8367 (mtp) REVERT: A 333 GLU cc_start: 0.7943 (tt0) cc_final: 0.7612 (tt0) REVERT: A 387 TRP cc_start: 0.7948 (t60) cc_final: 0.7538 (t-100) REVERT: A 413 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7658 (tttt) REVERT: A 456 VAL cc_start: 0.8300 (t) cc_final: 0.8046 (m) REVERT: A 475 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: A 482 TYR cc_start: 0.8176 (m-80) cc_final: 0.7934 (m-80) REVERT: B 100 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8053 (ttpt) REVERT: B 130 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7544 (mt0) REVERT: B 216 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8312 (mmm160) REVERT: B 219 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8074 (ptmm) REVERT: B 239 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: B 247 ASN cc_start: 0.8132 (t0) cc_final: 0.7801 (t0) REVERT: B 256 MET cc_start: 0.8734 (mtt) cc_final: 0.8407 (mtp) REVERT: B 267 GLU cc_start: 0.7976 (pp20) cc_final: 0.7696 (tm-30) REVERT: B 290 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7144 (tpm-80) REVERT: B 362 CYS cc_start: 0.8134 (m) cc_final: 0.7733 (m) REVERT: B 387 TRP cc_start: 0.7846 (t60) cc_final: 0.7352 (t-100) REVERT: B 413 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7719 (tttt) REVERT: B 475 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: B 482 TYR cc_start: 0.8173 (m-80) cc_final: 0.7913 (m-80) REVERT: C 36 SER cc_start: 0.9200 (p) cc_final: 0.8961 (m) REVERT: C 100 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8140 (ttpt) REVERT: C 216 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8377 (mmm160) REVERT: C 239 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8195 (mp10) REVERT: C 256 MET cc_start: 0.8620 (mtt) cc_final: 0.8354 (mtp) REVERT: C 333 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7724 (tt0) REVERT: C 362 CYS cc_start: 0.8019 (m) cc_final: 0.7746 (m) REVERT: C 387 TRP cc_start: 0.7897 (t60) cc_final: 0.7364 (t-100) REVERT: C 456 VAL cc_start: 0.8296 (t) cc_final: 0.8062 (m) REVERT: C 482 TYR cc_start: 0.8199 (m-80) cc_final: 0.7951 (m-80) REVERT: D 36 SER cc_start: 0.9164 (p) cc_final: 0.8917 (m) REVERT: D 100 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8094 (ttpt) REVERT: D 216 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8322 (mmm160) REVERT: D 239 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: D 247 ASN cc_start: 0.7961 (t0) cc_final: 0.7650 (t160) REVERT: D 256 MET cc_start: 0.8572 (mtt) cc_final: 0.8280 (mtp) REVERT: D 333 GLU cc_start: 0.7949 (tt0) cc_final: 0.7687 (tt0) REVERT: D 387 TRP cc_start: 0.7807 (t60) cc_final: 0.7373 (t-100) REVERT: D 413 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7205 (tttp) REVERT: D 475 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8263 (mt0) outliers start: 83 outliers final: 30 residues processed: 286 average time/residue: 1.6138 time to fit residues: 507.1688 Evaluate side-chains 249 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 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 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 105 GLU Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 149 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 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 C residue 100 LYS Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 489 VAL 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 174 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 191 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** ** 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 = 0.4096 r_free = 0.4096 target = 0.188101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.128658 restraints weight = 18027.390| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.07 r_work: 0.3189 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.004 0.052 18136 Z= 0.148 Angle : 0.674 12.479 24604 Z= 0.320 Chirality : 0.047 0.215 2760 Planarity : 0.005 0.056 3156 Dihedral : 9.299 127.758 2579 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.96 % Favored : 94.86 % Rotamer: Outliers : 4.17 % Allowed : 28.19 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2216 helix: 1.06 (0.17), residues: 952 sheet: 0.69 (0.27), residues: 388 loop : -1.98 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.004 0.001 HIS B 116 PHE 0.020 0.002 PHE D 167 TYR 0.013 0.001 TYR D 42 ARG 0.014 0.001 ARG C 498 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 684) hydrogen bonds : angle 4.56147 ( 2040) covalent geometry : bond 0.00354 (18136) covalent geometry : angle 0.67388 (24604) *********************** 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 287 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 206 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8046 (ttpt) REVERT: A 216 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8288 (mmm160) REVERT: A 239 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: A 247 ASN cc_start: 0.7830 (t0) cc_final: 0.7542 (t0) REVERT: A 256 MET cc_start: 0.8753 (mtt) cc_final: 0.8393 (mtp) REVERT: A 333 GLU cc_start: 0.7956 (tt0) cc_final: 0.7619 (tt0) REVERT: A 387 TRP cc_start: 0.7935 (t60) cc_final: 0.7510 (t-100) REVERT: A 475 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: A 482 TYR cc_start: 0.8229 (m-80) cc_final: 0.7963 (m-80) REVERT: B 100 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8047 (ttpt) REVERT: B 130 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7609 (mt0) REVERT: B 216 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8273 (mmm160) REVERT: B 219 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7987 (pttm) REVERT: B 239 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: B 247 ASN cc_start: 0.8109 (t0) cc_final: 0.7758 (t0) REVERT: B 256 MET cc_start: 0.8797 (mtt) cc_final: 0.8456 (mtp) REVERT: B 387 TRP cc_start: 0.7835 (t60) cc_final: 0.7381 (t-100) REVERT: B 413 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7717 (tttt) REVERT: B 475 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: B 482 TYR cc_start: 0.8193 (m-80) cc_final: 0.7915 (m-80) REVERT: C 100 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8104 (ttpt) REVERT: C 130 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: C 216 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8338 (mmm160) REVERT: C 239 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: C 256 MET cc_start: 0.8649 (mtt) cc_final: 0.8374 (mtp) REVERT: C 333 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7699 (tt0) REVERT: C 362 CYS cc_start: 0.8015 (m) cc_final: 0.7723 (m) REVERT: C 387 TRP cc_start: 0.7903 (t60) cc_final: 0.7360 (t-100) REVERT: C 482 TYR cc_start: 0.8213 (m-80) cc_final: 0.7946 (m-80) REVERT: D 100 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8082 (ttpt) REVERT: D 130 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: D 216 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8284 (mmm160) REVERT: D 239 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: D 247 ASN cc_start: 0.7976 (t0) cc_final: 0.7654 (t160) REVERT: D 256 MET cc_start: 0.8597 (mtt) cc_final: 0.8296 (mtp) REVERT: D 333 GLU cc_start: 0.7956 (tt0) cc_final: 0.7673 (tt0) REVERT: D 387 TRP cc_start: 0.7802 (t60) cc_final: 0.7351 (t-100) REVERT: D 475 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: D 550 ARG cc_start: 0.7758 (mmt-90) cc_final: 0.7498 (mtt-85) outliers start: 81 outliers final: 42 residues processed: 273 average time/residue: 2.3400 time to fit residues: 705.5475 Evaluate side-chains 261 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 199 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 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 433 VAL Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 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 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 492 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LYS Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 LYS Chi-restraints excluded: chain C residue 489 VAL 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 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 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 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2486 > 50: distance: 14 - 18: 4.097 distance: 18 - 19: 3.613 distance: 20 - 21: 6.334 distance: 20 - 24: 4.497 distance: 22 - 23: 4.733 distance: 24 - 25: 4.313 distance: 25 - 26: 4.263 distance: 25 - 28: 3.512 distance: 26 - 27: 8.402 distance: 26 - 32: 11.810 distance: 28 - 29: 7.682 distance: 29 - 30: 5.777 distance: 29 - 31: 7.689 distance: 32 - 33: 6.727 distance: 33 - 34: 9.081 distance: 33 - 36: 7.265 distance: 34 - 35: 12.000 distance: 34 - 40: 17.232 distance: 36 - 37: 11.473 distance: 37 - 38: 11.533 distance: 37 - 39: 17.949 distance: 40 - 41: 18.461 distance: 41 - 42: 9.256 distance: 41 - 44: 10.168 distance: 42 - 43: 29.555 distance: 42 - 49: 20.831 distance: 44 - 45: 8.874 distance: 45 - 46: 6.482 distance: 46 - 47: 3.145 distance: 46 - 48: 7.012 distance: 49 - 50: 10.852 distance: 50 - 51: 10.040 distance: 50 - 53: 12.605 distance: 51 - 52: 9.447 distance: 51 - 58: 6.437 distance: 52 - 82: 9.699 distance: 53 - 54: 4.698 distance: 54 - 55: 16.518 distance: 55 - 56: 14.130 distance: 55 - 57: 8.983 distance: 58 - 59: 6.905 distance: 59 - 60: 3.703 distance: 59 - 62: 4.505 distance: 60 - 61: 8.983 distance: 61 - 92: 13.445 distance: 62 - 63: 3.834 distance: 63 - 64: 4.204 distance: 64 - 65: 3.390 distance: 64 - 66: 5.533 distance: 68 - 71: 4.283 distance: 69 - 70: 4.110 distance: 69 - 74: 6.726 distance: 70 - 98: 5.213 distance: 71 - 72: 5.627 distance: 71 - 73: 8.183 distance: 74 - 75: 3.449 distance: 75 - 76: 7.237 distance: 76 - 77: 7.526 distance: 76 - 82: 8.437 distance: 78 - 79: 5.523 distance: 79 - 80: 3.243 distance: 79 - 81: 3.886 distance: 82 - 83: 7.635 distance: 83 - 84: 3.280 distance: 83 - 86: 4.550 distance: 84 - 85: 15.521 distance: 84 - 92: 6.167 distance: 86 - 87: 9.237 distance: 87 - 88: 7.301 distance: 87 - 89: 11.249 distance: 88 - 90: 7.442 distance: 89 - 91: 4.292 distance: 90 - 91: 8.143 distance: 92 - 93: 11.213 distance: 93 - 94: 14.133 distance: 94 - 95: 10.293 distance: 94 - 98: 11.943 distance: 96 - 97: 10.460