Starting phenix.real_space_refine on Sun Aug 24 02:49:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8has_34607/08_2025/8has_34607_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8has_34607/08_2025/8has_34607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8has_34607/08_2025/8has_34607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8has_34607/08_2025/8has_34607.map" model { file = "/net/cci-nas-00/data/ceres_data/8has_34607/08_2025/8has_34607_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8has_34607/08_2025/8has_34607_trim.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.107 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 66 5.16 5 C 10481 2.51 5 N 2877 2.21 5 O 3198 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16640 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2766 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 344} Chain breaks: 1 Chain: "B" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2745 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 341} Chain breaks: 1 Chain: "C" Number of atoms: 2757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2757 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2753 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342} Chain breaks: 1 Chain: "E" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2714 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 337} Chain breaks: 1 Chain: "F" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2719 Classifications: {'peptide': 354} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.43, per 1000 atoms: 0.27 Number of scatterers: 16640 At special positions: 0 Unit cell: (121.339, 120.266, 102.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 18 15.00 O 3198 8.00 N 2877 7.00 C 10481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 814.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 21 sheets defined 15.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.672A pdb=" N LEU A 108 " --> pdb=" O HIS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.608A pdb=" N CYS A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 302 through 306 Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.874A pdb=" N LEU A 331 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.674A pdb=" N ASP B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.761A pdb=" N THR B 305 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.795A pdb=" N LEU B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.667A pdb=" N SER B 449 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.938A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.713A pdb=" N ASP C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 327 through 331 removed outlier: 4.059A pdb=" N LEU C 331 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 439 removed outlier: 3.776A pdb=" N ARG C 438 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 434 through 439' Processing helix chain 'C' and resid 447 through 455 removed outlier: 4.225A pdb=" N GLN C 451 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 452 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA C 453 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN C 455 " --> pdb=" O GLN C 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.878A pdb=" N ILE D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.920A pdb=" N CYS D 150 " --> pdb=" O PRO D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 193 removed outlier: 3.754A pdb=" N ASP D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.946A pdb=" N THR D 305 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.948A pdb=" N LEU D 331 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 removed outlier: 3.504A pdb=" N ASP D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 removed outlier: 3.741A pdb=" N ILE E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 removed outlier: 3.668A pdb=" N ARG E 110 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE E 111 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER E 112 " --> pdb=" O ARG E 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 107 through 112' Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.662A pdb=" N CYS E 150 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.691A pdb=" N ASP E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 271 through 276 removed outlier: 3.660A pdb=" N TRP E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 331 removed outlier: 3.976A pdb=" N LEU E 331 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 438 Processing helix chain 'E' and resid 447 through 452 Processing helix chain 'F' and resid 93 through 104 removed outlier: 4.046A pdb=" N ILE F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 removed outlier: 3.654A pdb=" N ARG F 110 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE F 111 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER F 112 " --> pdb=" O ARG F 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 107 through 112' Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 186 through 193 removed outlier: 3.816A pdb=" N ASP F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 302 through 306 removed outlier: 3.825A pdb=" N THR F 305 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 331 removed outlier: 3.924A pdb=" N LEU F 331 " --> pdb=" O LEU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 413 removed outlier: 3.712A pdb=" N GLY F 413 " --> pdb=" O ALA F 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 413' Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 90 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 89 through 90 current: chain 'A' and resid 125 through 136 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 125 through 136 current: chain 'A' and resid 161 through 170 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 161 through 170 current: chain 'A' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 286 through 288 current: chain 'A' and resid 344 through 356 removed outlier: 5.477A pdb=" N THR A 349 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLY A 373 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET A 351 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 371 " --> pdb=" O MET A 351 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TYR A 353 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 369 " --> pdb=" O TYR A 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 364 through 373 current: chain 'A' and resid 401 through 405 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 401 through 405 current: chain 'A' and resid 424 through 431 Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.650A pdb=" N ARG A 265 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 292 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 245 through 249 removed outlier: 6.408A pdb=" N MET A 246 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 89 through 90 current: chain 'B' and resid 125 through 136 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 125 through 136 current: chain 'B' and resid 161 through 171 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 161 through 171 current: chain 'B' and resid 286 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 286 through 288 current: chain 'B' and resid 344 through 358 removed outlier: 5.491A pdb=" N THR B 349 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY B 373 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET B 351 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 371 " --> pdb=" O MET B 351 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR B 353 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 369 " --> pdb=" O TYR B 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 364 through 373 current: chain 'B' and resid 400 through 405 Processing sheet with id=AA5, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AA6, first strand: chain 'B' and resid 293 through 295 removed outlier: 3.626A pdb=" N LEU B 230 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B 216 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.541A pdb=" N MET B 246 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 122 removed outlier: 7.293A pdb=" N ALA C 116 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ALA C 131 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY C 118 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 129 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG C 120 " --> pdb=" O THR C 127 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 125 through 136 current: chain 'C' and resid 162 through 169 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 169 current: chain 'C' and resid 344 through 358 removed outlier: 5.573A pdb=" N THR C 349 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLY C 373 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET C 351 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL C 371 " --> pdb=" O MET C 351 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR C 353 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE C 369 " --> pdb=" O TYR C 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 364 through 373 current: chain 'C' and resid 400 through 405 Processing sheet with id=AA9, first strand: chain 'C' and resid 217 through 219 removed outlier: 4.253A pdb=" N GLY C 292 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 267 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 265 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 246 through 249 removed outlier: 6.406A pdb=" N MET C 246 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 89 through 90 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 89 through 90 current: chain 'D' and resid 125 through 136 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 136 current: chain 'D' and resid 161 through 169 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 161 through 169 current: chain 'D' and resid 286 through 289 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 286 through 289 current: chain 'D' and resid 344 through 358 removed outlier: 5.652A pdb=" N THR D 349 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY D 373 " --> pdb=" O THR D 349 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET D 351 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL D 371 " --> pdb=" O MET D 351 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR D 353 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 369 " --> pdb=" O TYR D 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 364 through 373 current: chain 'D' and resid 400 through 405 Processing sheet with id=AB3, first strand: chain 'D' and resid 216 through 219 removed outlier: 3.505A pdb=" N ALA D 216 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 245 through 249 removed outlier: 6.569A pdb=" N MET D 246 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 122 removed outlier: 6.863A pdb=" N GLY E 114 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU E 133 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ALA E 116 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA E 131 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLY E 118 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE E 129 " --> pdb=" O GLY E 118 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG E 120 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP E 125 " --> pdb=" O ARG E 122 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 125 through 136 current: chain 'E' and resid 161 through 171 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 161 through 171 current: chain 'E' and resid 344 through 357 removed outlier: 5.302A pdb=" N THR E 349 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLY E 373 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET E 351 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL E 371 " --> pdb=" O MET E 351 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR E 353 " --> pdb=" O ILE E 369 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 369 " --> pdb=" O TYR E 353 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 367 through 373 current: chain 'E' and resid 401 through 405 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 401 through 405 current: chain 'E' and resid 424 through 431 Processing sheet with id=AB6, first strand: chain 'E' and resid 217 through 219 removed outlier: 3.942A pdb=" N GLY E 292 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG E 265 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 245 through 249 removed outlier: 6.331A pdb=" N MET E 246 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 286 through 287 Processing sheet with id=AB9, first strand: chain 'F' and resid 89 through 90 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 89 through 90 current: chain 'F' and resid 125 through 136 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 125 through 136 current: chain 'F' and resid 161 through 171 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 161 through 171 current: chain 'F' and resid 344 through 358 removed outlier: 5.552A pdb=" N VAL F 350 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL F 372 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA F 352 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP F 368 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU F 356 " --> pdb=" O PHE F 366 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE F 366 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN F 358 " --> pdb=" O CYS F 364 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS F 364 " --> pdb=" O ASN F 358 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 364 through 373 current: chain 'F' and resid 401 through 408 Processing sheet with id=AC1, first strand: chain 'F' and resid 204 through 206 Processing sheet with id=AC2, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AC3, first strand: chain 'F' and resid 245 through 249 removed outlier: 6.610A pdb=" N MET F 246 " --> pdb=" O LEU F 260 " (cutoff:3.500A) 194 hydrogen bonds defined for protein. 501 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: 2.65 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2819 1.28 - 1.41: 4161 1.41 - 1.54: 9824 1.54 - 1.68: 89 1.68 - 1.81: 90 Bond restraints: 16983 Sorted by residual: bond pdb=" C5 ATP B 601 " pdb=" N7 ATP B 601 " ideal model delta sigma weight residual 1.387 1.258 0.129 1.00e-02 1.00e+04 1.65e+02 bond pdb=" C5 ATP D 601 " pdb=" N7 ATP D 601 " ideal model delta sigma weight residual 1.387 1.271 0.116 1.00e-02 1.00e+04 1.34e+02 bond pdb=" C5 ATP C 601 " pdb=" N7 ATP C 601 " ideal model delta sigma weight residual 1.387 1.272 0.115 1.00e-02 1.00e+04 1.33e+02 bond pdb=" C5 ATP F 601 " pdb=" N7 ATP F 601 " ideal model delta sigma weight residual 1.387 1.277 0.110 1.00e-02 1.00e+04 1.22e+02 bond pdb=" C5 ATP E 601 " pdb=" N7 ATP E 601 " ideal model delta sigma weight residual 1.387 1.288 0.099 1.00e-02 1.00e+04 9.84e+01 ... (remaining 16978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.42: 22899 5.42 - 10.85: 135 10.85 - 16.27: 40 16.27 - 21.69: 7 21.69 - 27.11: 6 Bond angle restraints: 23087 Sorted by residual: angle pdb=" C5' ATP A 601 " pdb=" O5' ATP A 601 " pdb=" PA ATP A 601 " ideal model delta sigma weight residual 121.27 107.32 13.95 1.00e+00 1.00e+00 1.95e+02 angle pdb=" C5' ATP E 601 " pdb=" O5' ATP E 601 " pdb=" PA ATP E 601 " ideal model delta sigma weight residual 121.27 107.37 13.90 1.00e+00 1.00e+00 1.93e+02 angle pdb=" N TYR A 241 " pdb=" CA TYR A 241 " pdb=" C TYR A 241 " ideal model delta sigma weight residual 110.39 93.48 16.91 1.30e+00 5.92e-01 1.69e+02 angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 124.10 12.73 1.00e+00 1.00e+00 1.62e+02 angle pdb=" C5 ATP C 601 " pdb=" C4 ATP C 601 " pdb=" N3 ATP C 601 " ideal model delta sigma weight residual 126.80 114.11 12.69 1.00e+00 1.00e+00 1.61e+02 ... (remaining 23082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8173 17.88 - 35.75: 1246 35.75 - 53.63: 502 53.63 - 71.50: 127 71.50 - 89.38: 33 Dihedral angle restraints: 10081 sinusoidal: 4093 harmonic: 5988 Sorted by residual: dihedral pdb=" CA LEU F 439 " pdb=" C LEU F 439 " pdb=" N GLU F 440 " pdb=" CA GLU F 440 " ideal model delta harmonic sigma weight residual 180.00 -141.09 -38.91 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" CA LEU C 439 " pdb=" C LEU C 439 " pdb=" N GLU C 440 " pdb=" CA GLU C 440 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA VAL C 288 " pdb=" C VAL C 288 " pdb=" N ARG C 289 " pdb=" CA ARG C 289 " ideal model delta harmonic sigma weight residual 180.00 147.34 32.66 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 10078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 2574 0.126 - 0.253: 20 0.253 - 0.379: 12 0.379 - 0.505: 3 0.505 - 0.631: 3 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA HIS F 233 " pdb=" N HIS F 233 " pdb=" C HIS F 233 " pdb=" CB HIS F 233 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.96e+00 chirality pdb=" CA HIS B 233 " pdb=" N HIS B 233 " pdb=" C HIS B 233 " pdb=" CB HIS B 233 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.49e+00 chirality pdb=" CA HIS C 233 " pdb=" N HIS C 233 " pdb=" C HIS C 233 " pdb=" CB HIS C 233 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.60e+00 ... (remaining 2609 not shown) Planarity restraints: 2974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 232 " 0.026 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C ASN C 232 " -0.086 2.00e-02 2.50e+03 pdb=" O ASN C 232 " 0.030 2.00e-02 2.50e+03 pdb=" N HIS C 233 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 238 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ASP A 238 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP A 238 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU A 239 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 231 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C THR E 231 " -0.054 2.00e-02 2.50e+03 pdb=" O THR E 231 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN E 232 " 0.019 2.00e-02 2.50e+03 ... (remaining 2971 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 775 2.69 - 3.24: 14458 3.24 - 3.80: 25125 3.80 - 4.35: 33657 4.35 - 4.90: 58026 Nonbonded interactions: 132041 Sorted by model distance: nonbonded pdb=" O LEU F 108 " pdb=" OG SER F 112 " model vdw 2.141 3.040 nonbonded pdb=" O THR B 305 " pdb=" OG1 THR B 305 " model vdw 2.171 3.040 nonbonded pdb=" OG SER D 393 " pdb=" O GLU D 397 " model vdw 2.179 3.040 nonbonded pdb=" N ASN D 224 " pdb=" OD1 ASN D 224 " model vdw 2.192 3.120 nonbonded pdb=" N ASN A 447 " pdb=" OD1 ASN A 447 " model vdw 2.195 3.120 ... (remaining 132036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 90 through 172 or resid 183 through 451 or resid 601)) selection = (chain 'B' and (resid 90 through 172 or resid 183 through 451 or resid 601)) selection = (chain 'C' and (resid 90 through 451 or resid 601)) selection = (chain 'D' and (resid 90 through 172 or resid 183 through 451 or resid 601)) selection = (chain 'E' and (resid 90 through 451 or resid 601)) selection = (chain 'F' and resid 90 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.520 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.009 0.163 16983 Z= 0.586 Angle : 1.226 27.114 23087 Z= 0.775 Chirality : 0.055 0.631 2612 Planarity : 0.005 0.060 2974 Dihedral : 20.793 89.376 6265 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.92 % Favored : 95.65 % Rotamer: Outliers : 6.98 % Allowed : 37.97 % Favored : 55.05 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.18), residues: 2117 helix: -2.05 (0.35), residues: 208 sheet: -1.29 (0.22), residues: 522 loop : -1.18 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 438 TYR 0.016 0.001 TYR B 241 PHE 0.026 0.001 PHE F 111 TRP 0.019 0.001 TRP F 426 HIS 0.020 0.002 HIS F 233 Details of bonding type rmsd covalent geometry : bond 0.00866 (16983) covalent geometry : angle 1.22617 (23087) hydrogen bonds : bond 0.29874 ( 194) hydrogen bonds : angle 9.52387 ( 501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 180 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8496 (pttp) cc_final: 0.8018 (pptt) REVERT: A 240 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6375 (p0) REVERT: D 110 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7636 (ptp-170) REVERT: D 142 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7828 (ptmm) REVERT: D 415 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7944 (tp) REVERT: E 142 LYS cc_start: 0.8094 (tttp) cc_final: 0.7643 (tmmt) REVERT: E 245 LYS cc_start: 0.7292 (mttp) cc_final: 0.7056 (mmtp) REVERT: F 239 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5735 (tt) REVERT: F 415 LEU cc_start: 0.8092 (tt) cc_final: 0.7530 (tt) outliers start: 125 outliers final: 105 residues processed: 302 average time/residue: 0.4665 time to fit residues: 162.2487 Evaluate side-chains 272 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 163 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 416 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 377 GLN Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 170 PHE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 447 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 421 HIS C 335 GLN D 233 HIS E 224 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 HIS F 244 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.195189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162712 restraints weight = 19225.674| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.59 r_work: 0.3671 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16983 Z= 0.114 Angle : 0.580 10.992 23087 Z= 0.303 Chirality : 0.045 0.297 2612 Planarity : 0.004 0.050 2974 Dihedral : 13.477 89.260 2684 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.01 % Favored : 94.80 % Rotamer: Outliers : 8.93 % Allowed : 33.05 % Favored : 58.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.18), residues: 2117 helix: -2.02 (0.34), residues: 221 sheet: -1.10 (0.22), residues: 487 loop : -1.15 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 438 TYR 0.009 0.001 TYR F 241 PHE 0.018 0.001 PHE D 170 TRP 0.014 0.001 TRP A 406 HIS 0.011 0.001 HIS E 233 Details of bonding type rmsd covalent geometry : bond 0.00255 (16983) covalent geometry : angle 0.57962 (23087) hydrogen bonds : bond 0.03926 ( 194) hydrogen bonds : angle 6.55542 ( 501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 197 time to evaluate : 0.754 Fit side-chains REVERT: A 98 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7398 (mtp) REVERT: A 142 LYS cc_start: 0.8254 (pttp) cc_final: 0.7600 (pptt) REVERT: A 240 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6368 (p0) REVERT: A 254 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 324 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7506 (tp) REVERT: A 328 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7357 (tt) REVERT: B 109 ARG cc_start: 0.7751 (ptt180) cc_final: 0.7328 (ptm160) REVERT: B 244 GLN cc_start: 0.6492 (mp10) cc_final: 0.5993 (mm110) REVERT: B 254 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8242 (tt) REVERT: B 338 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8248 (pttp) REVERT: C 112 SER cc_start: 0.8753 (p) cc_final: 0.8437 (m) REVERT: C 254 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8241 (tt) REVERT: C 374 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: D 184 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7206 (mmm) REVERT: D 220 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6314 (mmt90) REVERT: D 358 ASN cc_start: 0.6089 (OUTLIER) cc_final: 0.5723 (m110) REVERT: D 377 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7195 (mt0) REVERT: D 382 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7778 (tm-30) REVERT: D 442 ASP cc_start: 0.7539 (t0) cc_final: 0.7332 (t0) REVERT: E 138 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7612 (ttt-90) REVERT: E 142 LYS cc_start: 0.7474 (tttp) cc_final: 0.6865 (tmmt) REVERT: E 245 LYS cc_start: 0.7154 (mttp) cc_final: 0.6929 (mmtp) REVERT: E 254 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8106 (tt) REVERT: E 328 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7262 (tt) REVERT: E 414 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6714 (mtp85) REVERT: F 241 TYR cc_start: 0.1908 (OUTLIER) cc_final: 0.0093 (m-80) REVERT: F 254 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8175 (tt) outliers start: 160 outliers final: 79 residues processed: 326 average time/residue: 0.5227 time to fit residues: 192.2525 Evaluate side-chains 265 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 167 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 377 GLN Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain E residue 170 PHE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 414 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 0.4980 chunk 98 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 335 GLN D 224 ASN D 233 HIS D 244 GLN E 224 ASN E 233 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.187604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153915 restraints weight = 19230.091| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.59 r_work: 0.3562 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16983 Z= 0.147 Angle : 0.615 11.373 23087 Z= 0.319 Chirality : 0.047 0.280 2612 Planarity : 0.004 0.052 2974 Dihedral : 12.159 80.204 2594 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.67 % Favored : 94.14 % Rotamer: Outliers : 9.10 % Allowed : 31.99 % Favored : 58.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.17), residues: 2117 helix: -2.05 (0.32), residues: 227 sheet: -1.35 (0.22), residues: 469 loop : -1.21 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 438 TYR 0.012 0.001 TYR C 259 PHE 0.023 0.001 PHE D 170 TRP 0.015 0.001 TRP A 406 HIS 0.011 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00345 (16983) covalent geometry : angle 0.61531 (23087) hydrogen bonds : bond 0.03916 ( 194) hydrogen bonds : angle 6.16353 ( 501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 177 time to evaluate : 0.580 Fit side-chains REVERT: A 98 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7436 (mtp) REVERT: A 142 LYS cc_start: 0.8218 (pttp) cc_final: 0.7640 (pptt) REVERT: A 234 HIS cc_start: 0.7613 (m90) cc_final: 0.7210 (m90) REVERT: A 240 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6261 (p0) REVERT: A 328 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 414 ARG cc_start: 0.6997 (mtm180) cc_final: 0.6454 (mtp180) REVERT: A 438 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.5798 (tpp-160) REVERT: B 109 ARG cc_start: 0.7856 (ptt180) cc_final: 0.7381 (ptm160) REVERT: B 241 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.4189 (t80) REVERT: B 244 GLN cc_start: 0.7130 (mp10) cc_final: 0.6453 (mm110) REVERT: B 254 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8163 (tt) REVERT: B 338 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8319 (pttp) REVERT: C 254 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8178 (tt) REVERT: C 302 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: C 338 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8052 (pttm) REVERT: C 382 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 438 ARG cc_start: 0.6562 (mmt90) cc_final: 0.6013 (mpt180) REVERT: D 142 LYS cc_start: 0.7557 (ptmm) cc_final: 0.7258 (pptt) REVERT: D 220 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6017 (mmt90) REVERT: D 377 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: D 382 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7762 (tm-30) REVERT: D 442 ASP cc_start: 0.7534 (t0) cc_final: 0.7296 (t0) REVERT: E 138 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7751 (ttt-90) REVERT: E 142 LYS cc_start: 0.7609 (tttp) cc_final: 0.6962 (tmmt) REVERT: E 254 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7990 (tt) REVERT: E 328 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7676 (tt) REVERT: E 414 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6915 (mtp85) REVERT: F 98 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7632 (mtp) REVERT: F 107 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8247 (pt) REVERT: F 221 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6540 (mtm180) REVERT: F 241 TYR cc_start: 0.2268 (OUTLIER) cc_final: -0.0217 (m-80) REVERT: F 254 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8148 (tt) REVERT: F 415 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8362 (tp) outliers start: 163 outliers final: 81 residues processed: 312 average time/residue: 0.5344 time to fit residues: 187.4137 Evaluate side-chains 268 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 165 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 438 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 377 GLN Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 414 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 221 ARG Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 160 optimal weight: 7.9990 chunk 78 optimal weight: 0.1980 chunk 114 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 233 HIS C 335 GLN D 233 HIS D 244 GLN E 224 ASN E 233 HIS ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.187242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.153824 restraints weight = 19081.343| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.59 r_work: 0.3561 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16983 Z= 0.130 Angle : 0.585 11.738 23087 Z= 0.302 Chirality : 0.046 0.232 2612 Planarity : 0.004 0.050 2974 Dihedral : 11.171 85.084 2576 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 7.87 % Allowed : 32.83 % Favored : 59.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.17), residues: 2117 helix: -1.93 (0.33), residues: 226 sheet: -1.32 (0.22), residues: 478 loop : -1.13 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 221 TYR 0.012 0.001 TYR E 357 PHE 0.019 0.001 PHE D 170 TRP 0.014 0.001 TRP A 406 HIS 0.011 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00300 (16983) covalent geometry : angle 0.58470 (23087) hydrogen bonds : bond 0.03293 ( 194) hydrogen bonds : angle 5.95485 ( 501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 181 time to evaluate : 0.645 Fit side-chains REVERT: A 98 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7361 (mtp) REVERT: A 142 LYS cc_start: 0.8173 (pttp) cc_final: 0.7589 (pptt) REVERT: A 234 HIS cc_start: 0.7507 (m90) cc_final: 0.7073 (m90) REVERT: A 240 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6133 (p0) REVERT: A 245 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8228 (mmtp) REVERT: A 254 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8109 (tt) REVERT: A 265 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5967 (ttt-90) REVERT: A 328 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7659 (tt) REVERT: A 361 LYS cc_start: 0.6358 (mttt) cc_final: 0.6041 (mttm) REVERT: A 382 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 109 ARG cc_start: 0.7837 (ptt180) cc_final: 0.7388 (ptm160) REVERT: B 241 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.4198 (t80) REVERT: B 244 GLN cc_start: 0.7050 (mp10) cc_final: 0.6518 (mm110) REVERT: B 254 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8212 (tt) REVERT: B 338 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8201 (pttp) REVERT: B 414 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7818 (mtt180) REVERT: C 254 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8211 (tt) REVERT: C 302 ASP cc_start: 0.7091 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: C 338 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8179 (pttm) REVERT: C 382 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7971 (tm-30) REVERT: C 438 ARG cc_start: 0.6593 (mmt90) cc_final: 0.6114 (mpt180) REVERT: D 142 LYS cc_start: 0.7504 (ptmm) cc_final: 0.7181 (pptt) REVERT: D 184 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7391 (mmm) REVERT: D 220 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6003 (mmt90) REVERT: D 234 HIS cc_start: 0.7280 (m90) cc_final: 0.7073 (m90) REVERT: D 382 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7842 (tm-30) REVERT: D 414 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7638 (ttp80) REVERT: E 138 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7797 (ttt-90) REVERT: E 142 LYS cc_start: 0.7522 (tttp) cc_final: 0.6906 (tmmt) REVERT: E 254 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8010 (tt) REVERT: E 328 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7631 (tt) REVERT: E 412 ARG cc_start: 0.4004 (OUTLIER) cc_final: 0.3692 (mtm180) REVERT: E 414 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6740 (mtp85) REVERT: F 98 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7515 (mtp) REVERT: F 221 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6379 (mtm180) REVERT: F 230 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7971 (pt) REVERT: F 241 TYR cc_start: 0.1759 (OUTLIER) cc_final: 0.1522 (m-80) REVERT: F 254 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8126 (tt) REVERT: F 338 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8307 (pttp) outliers start: 141 outliers final: 72 residues processed: 297 average time/residue: 0.5114 time to fit residues: 170.0445 Evaluate side-chains 266 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 167 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 412 ARG Chi-restraints excluded: chain E residue 414 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 221 ARG Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 122 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 177 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 21 optimal weight: 0.1980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 226 GLN B 233 HIS C 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 HIS ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.185007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150888 restraints weight = 18913.720| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.61 r_work: 0.3528 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16983 Z= 0.161 Angle : 0.625 11.865 23087 Z= 0.322 Chirality : 0.047 0.268 2612 Planarity : 0.004 0.050 2974 Dihedral : 11.292 87.436 2567 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.86 % Favored : 94.00 % Rotamer: Outliers : 9.16 % Allowed : 31.99 % Favored : 58.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.17), residues: 2117 helix: -1.97 (0.32), residues: 228 sheet: -1.26 (0.22), residues: 480 loop : -1.13 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 221 TYR 0.014 0.001 TYR E 357 PHE 0.021 0.002 PHE D 170 TRP 0.012 0.001 TRP A 406 HIS 0.012 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00383 (16983) covalent geometry : angle 0.62505 (23087) hydrogen bonds : bond 0.03669 ( 194) hydrogen bonds : angle 6.02509 ( 501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 179 time to evaluate : 0.657 Fit side-chains REVERT: A 98 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7597 (mtp) REVERT: A 142 LYS cc_start: 0.8195 (pttp) cc_final: 0.7663 (pptt) REVERT: A 219 LYS cc_start: 0.7132 (ttpp) cc_final: 0.6809 (ttmm) REVERT: A 234 HIS cc_start: 0.7514 (m90) cc_final: 0.7124 (m90) REVERT: A 240 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6311 (p0) REVERT: A 245 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8283 (mmtp) REVERT: A 254 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 265 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.6075 (ttt-90) REVERT: A 328 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7713 (tt) REVERT: B 109 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7434 (ptm160) REVERT: B 142 LYS cc_start: 0.7347 (tmmt) cc_final: 0.6834 (tmmt) REVERT: B 241 TYR cc_start: 0.5014 (OUTLIER) cc_final: 0.4123 (t80) REVERT: B 244 GLN cc_start: 0.7442 (mp10) cc_final: 0.6723 (mm110) REVERT: B 254 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8146 (tt) REVERT: B 338 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8526 (pttp) REVERT: B 376 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8107 (mtp-110) REVERT: B 414 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7772 (mtt180) REVERT: C 254 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8162 (tt) REVERT: C 338 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8188 (pttp) REVERT: C 382 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7884 (tm-30) REVERT: C 438 ARG cc_start: 0.6448 (mmt90) cc_final: 0.6061 (mpt180) REVERT: D 142 LYS cc_start: 0.7451 (ptmm) cc_final: 0.7184 (pptt) REVERT: D 184 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7262 (mmm) REVERT: D 220 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6237 (mmt90) REVERT: D 246 MET cc_start: 0.8625 (mmp) cc_final: 0.8400 (mmt) REVERT: D 414 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7790 (ttp80) REVERT: E 92 ASN cc_start: 0.7326 (p0) cc_final: 0.6977 (t0) REVERT: E 138 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7853 (ttt-90) REVERT: E 142 LYS cc_start: 0.7651 (tttp) cc_final: 0.6944 (tmmt) REVERT: E 172 TYR cc_start: 0.6334 (t80) cc_final: 0.6039 (t80) REVERT: E 234 HIS cc_start: 0.7245 (m90) cc_final: 0.6836 (m90) REVERT: E 254 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7994 (tt) REVERT: E 328 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7746 (tt) REVERT: E 378 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8119 (t) REVERT: E 417 LEU cc_start: 0.4146 (OUTLIER) cc_final: 0.3818 (tt) REVERT: F 98 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7599 (mtp) REVERT: F 221 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6182 (mtm180) REVERT: F 230 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7980 (pt) REVERT: F 241 TYR cc_start: 0.1944 (OUTLIER) cc_final: -0.0738 (m-80) REVERT: F 254 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8085 (tt) REVERT: F 338 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8329 (pttp) REVERT: F 414 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6515 (ttp80) outliers start: 164 outliers final: 91 residues processed: 316 average time/residue: 0.5044 time to fit residues: 179.1726 Evaluate side-chains 276 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 158 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 378 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 221 ARG Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 241 TYR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 425 ASN Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 102 optimal weight: 0.0270 chunk 50 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 201 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 200 optimal weight: 0.0970 chunk 196 optimal weight: 9.9990 overall best weight: 1.1838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 233 HIS C 335 GLN C 421 HIS D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 HIS E 244 GLN E 447 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155064 restraints weight = 19006.554| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.56 r_work: 0.3570 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16983 Z= 0.113 Angle : 0.565 10.842 23087 Z= 0.292 Chirality : 0.045 0.251 2612 Planarity : 0.004 0.049 2974 Dihedral : 10.456 84.066 2562 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.29 % Favored : 94.57 % Rotamer: Outliers : 7.54 % Allowed : 34.06 % Favored : 58.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.18), residues: 2117 helix: -1.74 (0.33), residues: 226 sheet: -1.13 (0.22), residues: 512 loop : -1.00 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 221 TYR 0.011 0.001 TYR E 357 PHE 0.020 0.001 PHE F 111 TRP 0.012 0.001 TRP A 406 HIS 0.012 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00259 (16983) covalent geometry : angle 0.56485 (23087) hydrogen bonds : bond 0.02954 ( 194) hydrogen bonds : angle 5.76780 ( 501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 179 time to evaluate : 0.478 Fit side-chains REVERT: A 98 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: A 142 LYS cc_start: 0.8134 (pttp) cc_final: 0.7633 (pptt) REVERT: A 219 LYS cc_start: 0.7149 (ttpp) cc_final: 0.6876 (ttmt) REVERT: A 234 HIS cc_start: 0.7451 (m90) cc_final: 0.7090 (m90) REVERT: A 240 ASP cc_start: 0.6622 (OUTLIER) cc_final: 0.6162 (p0) REVERT: A 254 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8076 (tt) REVERT: A 265 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6017 (ttt-90) REVERT: A 414 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6103 (ptm-80) REVERT: B 109 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7421 (ptm160) REVERT: B 142 LYS cc_start: 0.7409 (tmmt) cc_final: 0.6730 (tmmt) REVERT: B 219 LYS cc_start: 0.7230 (mtmm) cc_final: 0.7001 (ptpt) REVERT: B 241 TYR cc_start: 0.5010 (OUTLIER) cc_final: 0.4121 (t80) REVERT: B 244 GLN cc_start: 0.7389 (mp10) cc_final: 0.6746 (mm110) REVERT: B 254 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 338 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8476 (pttp) REVERT: B 376 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.8072 (mtp-110) REVERT: B 414 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7765 (mtt180) REVERT: C 254 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8256 (tt) REVERT: C 338 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8006 (pttp) REVERT: C 382 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7967 (tm-30) REVERT: C 438 ARG cc_start: 0.6410 (mmt90) cc_final: 0.6009 (mpt180) REVERT: D 142 LYS cc_start: 0.7434 (ptmm) cc_final: 0.7152 (pptt) REVERT: D 220 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6220 (mmt90) REVERT: D 254 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8207 (tt) REVERT: D 341 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8427 (ptm160) REVERT: D 382 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7831 (tm-30) REVERT: D 442 ASP cc_start: 0.7355 (t0) cc_final: 0.7130 (t0) REVERT: E 138 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7837 (ttt-90) REVERT: E 142 LYS cc_start: 0.7592 (tttp) cc_final: 0.6962 (tmmt) REVERT: E 234 HIS cc_start: 0.7152 (m90) cc_final: 0.6926 (m90) REVERT: E 254 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8110 (tt) REVERT: E 324 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7443 (tp) REVERT: E 328 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7720 (tt) REVERT: F 98 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7539 (mtp) REVERT: F 183 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: F 221 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6398 (mtm180) REVERT: F 239 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5616 (tt) REVERT: F 254 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8162 (tt) REVERT: F 278 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7139 (tp) REVERT: F 338 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8302 (pttp) REVERT: F 349 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8420 (m) REVERT: F 420 ASP cc_start: 0.6491 (p0) cc_final: 0.6084 (p0) outliers start: 135 outliers final: 64 residues processed: 294 average time/residue: 0.4949 time to fit residues: 162.2084 Evaluate side-chains 257 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 166 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 183 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 221 ARG Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 80 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 200 optimal weight: 0.0070 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.186861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152744 restraints weight = 18881.713| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.61 r_work: 0.3549 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16983 Z= 0.128 Angle : 0.580 11.009 23087 Z= 0.299 Chirality : 0.046 0.286 2612 Planarity : 0.004 0.048 2974 Dihedral : 10.090 75.928 2551 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 7.48 % Allowed : 33.61 % Favored : 58.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.18), residues: 2117 helix: -1.70 (0.33), residues: 227 sheet: -1.16 (0.22), residues: 489 loop : -0.98 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 412 TYR 0.013 0.001 TYR E 357 PHE 0.020 0.001 PHE F 111 TRP 0.011 0.001 TRP D 406 HIS 0.012 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00300 (16983) covalent geometry : angle 0.58033 (23087) hydrogen bonds : bond 0.03111 ( 194) hydrogen bonds : angle 5.76331 ( 501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 174 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7633 (mtp) REVERT: A 142 LYS cc_start: 0.8112 (pttp) cc_final: 0.7615 (pptt) REVERT: A 219 LYS cc_start: 0.7046 (ttpp) cc_final: 0.6762 (ttmm) REVERT: A 234 HIS cc_start: 0.7420 (m90) cc_final: 0.7006 (m90) REVERT: A 254 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8108 (tt) REVERT: A 265 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6018 (ttt-90) REVERT: A 328 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7702 (tt) REVERT: A 440 GLU cc_start: 0.6327 (tp30) cc_final: 0.6063 (tp30) REVERT: B 109 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7410 (ptm160) REVERT: B 142 LYS cc_start: 0.7429 (tmmt) cc_final: 0.6771 (tmmt) REVERT: B 241 TYR cc_start: 0.5038 (OUTLIER) cc_final: 0.4110 (t80) REVERT: B 244 GLN cc_start: 0.7455 (mp10) cc_final: 0.6754 (mm110) REVERT: B 254 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8100 (tt) REVERT: B 338 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8497 (pttp) REVERT: B 376 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8086 (mtp-110) REVERT: B 414 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7759 (mtt180) REVERT: C 219 LYS cc_start: 0.7203 (ttpp) cc_final: 0.6820 (ttmm) REVERT: C 254 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8162 (tt) REVERT: C 338 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8136 (pttm) REVERT: C 382 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 438 ARG cc_start: 0.6413 (mmt90) cc_final: 0.5988 (mpt180) REVERT: D 142 LYS cc_start: 0.7407 (ptmm) cc_final: 0.7167 (pptt) REVERT: D 220 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6216 (mmt90) REVERT: D 254 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8134 (tt) REVERT: D 341 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8442 (ptm160) REVERT: D 382 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7786 (tm-30) REVERT: D 442 ASP cc_start: 0.7336 (t0) cc_final: 0.7081 (t0) REVERT: E 92 ASN cc_start: 0.7348 (p0) cc_final: 0.7022 (t0) REVERT: E 138 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7831 (ttt-90) REVERT: E 142 LYS cc_start: 0.7582 (tttp) cc_final: 0.6910 (tmmt) REVERT: E 234 HIS cc_start: 0.7093 (m90) cc_final: 0.6835 (m90) REVERT: E 254 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8089 (tt) REVERT: E 328 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7719 (tt) REVERT: E 414 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6911 (mtp85) REVERT: F 98 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: F 183 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: F 221 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6339 (mtm180) REVERT: F 254 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8117 (tt) REVERT: F 278 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7090 (tp) REVERT: F 338 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8299 (pttp) REVERT: F 420 ASP cc_start: 0.6474 (p0) cc_final: 0.6054 (p0) outliers start: 134 outliers final: 73 residues processed: 288 average time/residue: 0.5045 time to fit residues: 162.5226 Evaluate side-chains 261 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 164 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 414 ARG Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 183 GLN Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 221 ARG Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 6 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 411 ASN B 233 HIS C 183 GLN C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148424 restraints weight = 18953.000| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.60 r_work: 0.3497 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16983 Z= 0.207 Angle : 0.682 11.288 23087 Z= 0.349 Chirality : 0.049 0.326 2612 Planarity : 0.005 0.049 2974 Dihedral : 10.892 76.717 2541 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 9.05 % Allowed : 32.27 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.17), residues: 2117 helix: -1.96 (0.31), residues: 230 sheet: -1.19 (0.23), residues: 470 loop : -1.10 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 412 TYR 0.020 0.002 TYR F 241 PHE 0.022 0.002 PHE D 170 TRP 0.016 0.002 TRP A 406 HIS 0.013 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00501 (16983) covalent geometry : angle 0.68233 (23087) hydrogen bonds : bond 0.03972 ( 194) hydrogen bonds : angle 6.12449 ( 501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 164 time to evaluate : 0.616 Fit side-chains REVERT: A 98 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7604 (mtp) REVERT: A 142 LYS cc_start: 0.8190 (pttp) cc_final: 0.7676 (pptt) REVERT: A 234 HIS cc_start: 0.7476 (m90) cc_final: 0.7063 (m90) REVERT: A 241 TYR cc_start: 0.5731 (OUTLIER) cc_final: 0.4377 (t80) REVERT: A 265 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6135 (ttt-90) REVERT: A 328 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7756 (tt) REVERT: A 367 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8125 (m) REVERT: A 414 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6328 (ptm-80) REVERT: A 440 GLU cc_start: 0.6305 (tp30) cc_final: 0.6079 (tp30) REVERT: B 142 LYS cc_start: 0.7562 (tmmt) cc_final: 0.6959 (tmmt) REVERT: B 241 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.3970 (t80) REVERT: B 244 GLN cc_start: 0.7586 (mp10) cc_final: 0.6846 (mm110) REVERT: B 254 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8053 (tt) REVERT: B 338 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8487 (pttm) REVERT: B 376 ARG cc_start: 0.8269 (mtp-110) cc_final: 0.8038 (mtp-110) REVERT: B 414 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7735 (mtt180) REVERT: C 142 LYS cc_start: 0.7681 (pptt) cc_final: 0.7314 (tttp) REVERT: C 219 LYS cc_start: 0.7185 (ttpp) cc_final: 0.6835 (ttmm) REVERT: C 254 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 338 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8053 (pttm) REVERT: C 382 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 438 ARG cc_start: 0.6635 (mmt90) cc_final: 0.6206 (mpt180) REVERT: D 142 LYS cc_start: 0.7470 (ptmm) cc_final: 0.7149 (pptt) REVERT: D 184 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7240 (mmm) REVERT: D 220 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6303 (mmt90) REVERT: D 382 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7686 (tm-30) REVERT: E 138 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7872 (ttt-90) REVERT: E 142 LYS cc_start: 0.7619 (tttp) cc_final: 0.6948 (tmmt) REVERT: E 234 HIS cc_start: 0.7407 (m90) cc_final: 0.7016 (m90) REVERT: E 328 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7844 (tt) REVERT: E 414 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7128 (mtp85) REVERT: F 221 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6361 (mtm180) REVERT: F 278 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7100 (tp) REVERT: F 338 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8368 (pttp) outliers start: 162 outliers final: 96 residues processed: 302 average time/residue: 0.5226 time to fit residues: 177.1139 Evaluate side-chains 269 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 153 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 357 TYR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 273 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 414 ARG Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 221 ARG Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 325 GLN Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 10 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 161 optimal weight: 0.0030 chunk 92 optimal weight: 0.0170 chunk 209 optimal weight: 0.0070 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 62 optimal weight: 0.0870 chunk 90 optimal weight: 8.9990 overall best weight: 0.8226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 411 ASN B 233 HIS B 421 HIS C 335 GLN C 421 HIS D 233 HIS D 283 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154802 restraints weight = 18913.471| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.62 r_work: 0.3572 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16983 Z= 0.104 Angle : 0.561 11.341 23087 Z= 0.288 Chirality : 0.045 0.287 2612 Planarity : 0.004 0.046 2974 Dihedral : 9.676 74.597 2541 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 5.25 % Allowed : 35.96 % Favored : 58.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 2117 helix: -1.57 (0.33), residues: 225 sheet: -1.08 (0.22), residues: 496 loop : -0.95 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 412 TYR 0.011 0.001 TYR E 357 PHE 0.024 0.001 PHE B 269 TRP 0.013 0.001 TRP F 406 HIS 0.012 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00238 (16983) covalent geometry : angle 0.56123 (23087) hydrogen bonds : bond 0.02653 ( 194) hydrogen bonds : angle 5.74689 ( 501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 177 time to evaluate : 0.638 Fit side-chains REVERT: A 98 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7658 (mtp) REVERT: A 142 LYS cc_start: 0.8085 (pttp) cc_final: 0.7591 (pptt) REVERT: A 172 TYR cc_start: 0.4236 (OUTLIER) cc_final: 0.3933 (m-80) REVERT: A 219 LYS cc_start: 0.6981 (ttpp) cc_final: 0.6702 (ttmm) REVERT: A 234 HIS cc_start: 0.7362 (m90) cc_final: 0.6992 (m90) REVERT: A 241 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.4299 (t80) REVERT: A 254 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8094 (tt) REVERT: A 265 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.6006 (ttt-90) REVERT: B 89 GLN cc_start: 0.7511 (tp40) cc_final: 0.6006 (tm-30) REVERT: B 109 ARG cc_start: 0.7931 (ptt180) cc_final: 0.7521 (ptm160) REVERT: B 142 LYS cc_start: 0.7443 (tmmt) cc_final: 0.6844 (tmmt) REVERT: B 241 TYR cc_start: 0.4690 (OUTLIER) cc_final: 0.3835 (t80) REVERT: B 244 GLN cc_start: 0.7399 (mp10) cc_final: 0.6739 (mm110) REVERT: B 254 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8086 (tt) REVERT: C 142 LYS cc_start: 0.7552 (pptt) cc_final: 0.7313 (tttp) REVERT: C 219 LYS cc_start: 0.7108 (ttpp) cc_final: 0.6789 (ttmm) REVERT: C 254 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8154 (tt) REVERT: C 338 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7957 (pttp) REVERT: C 382 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7921 (tm-30) REVERT: D 142 LYS cc_start: 0.7368 (ptmm) cc_final: 0.7107 (pptt) REVERT: D 220 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.5878 (mmt90) REVERT: D 254 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8052 (tt) REVERT: D 414 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7339 (tpt-90) REVERT: E 142 LYS cc_start: 0.7620 (tttp) cc_final: 0.7011 (tmmt) REVERT: E 234 HIS cc_start: 0.7013 (m90) cc_final: 0.6691 (m90) REVERT: E 254 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8057 (tt) REVERT: F 254 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8007 (tt) REVERT: F 278 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7055 (tp) REVERT: F 338 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8283 (pttp) REVERT: F 349 THR cc_start: 0.8664 (t) cc_final: 0.8411 (m) REVERT: F 420 ASP cc_start: 0.6419 (p0) cc_final: 0.6003 (p0) outliers start: 94 outliers final: 54 residues processed: 259 average time/residue: 0.5567 time to fit residues: 161.2723 Evaluate side-chains 228 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 158 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 132 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 233 HIS B 325 GLN C 335 GLN D 233 HIS E 233 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.187145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153158 restraints weight = 19003.947| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.62 r_work: 0.3555 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16983 Z= 0.122 Angle : 0.582 11.035 23087 Z= 0.297 Chirality : 0.046 0.324 2612 Planarity : 0.004 0.050 2974 Dihedral : 9.498 75.027 2537 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.76 % Favored : 94.10 % Rotamer: Outliers : 4.80 % Allowed : 36.29 % Favored : 58.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.18), residues: 2117 helix: -1.51 (0.33), residues: 228 sheet: -1.07 (0.22), residues: 477 loop : -0.91 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 412 TYR 0.012 0.001 TYR E 357 PHE 0.021 0.001 PHE F 111 TRP 0.013 0.001 TRP F 406 HIS 0.013 0.002 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00286 (16983) covalent geometry : angle 0.58205 (23087) hydrogen bonds : bond 0.02939 ( 194) hydrogen bonds : angle 5.71764 ( 501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 164 time to evaluate : 0.450 Fit side-chains REVERT: A 98 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7668 (mtp) REVERT: A 142 LYS cc_start: 0.8089 (pttp) cc_final: 0.7616 (pptt) REVERT: A 172 TYR cc_start: 0.4134 (OUTLIER) cc_final: 0.3804 (m-80) REVERT: A 219 LYS cc_start: 0.6966 (ttpp) cc_final: 0.6690 (ttmm) REVERT: A 234 HIS cc_start: 0.7376 (m90) cc_final: 0.6970 (m90) REVERT: A 241 TYR cc_start: 0.5580 (OUTLIER) cc_final: 0.4280 (t80) REVERT: A 254 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8063 (tt) REVERT: A 265 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6019 (ttt-90) REVERT: B 89 GLN cc_start: 0.7505 (tp40) cc_final: 0.5964 (tm-30) REVERT: B 109 ARG cc_start: 0.8148 (ptt180) cc_final: 0.7579 (ptm160) REVERT: B 142 LYS cc_start: 0.7521 (tmmt) cc_final: 0.6950 (tmmt) REVERT: B 241 TYR cc_start: 0.4773 (OUTLIER) cc_final: 0.3928 (t80) REVERT: B 244 GLN cc_start: 0.7426 (mp10) cc_final: 0.6751 (mm110) REVERT: B 254 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8060 (tt) REVERT: C 142 LYS cc_start: 0.7558 (pptt) cc_final: 0.7354 (tttp) REVERT: C 219 LYS cc_start: 0.7137 (ttpp) cc_final: 0.6810 (ttmm) REVERT: C 230 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7898 (pt) REVERT: C 254 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8115 (tt) REVERT: C 338 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7900 (pttm) REVERT: C 382 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8022 (tm-30) REVERT: C 438 ARG cc_start: 0.6441 (mmt90) cc_final: 0.5927 (mpt180) REVERT: D 142 LYS cc_start: 0.7347 (ptmm) cc_final: 0.7079 (pptt) REVERT: D 220 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6183 (mmt90) REVERT: D 254 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8074 (tt) REVERT: D 349 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8375 (m) REVERT: D 382 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7704 (tm-30) REVERT: D 414 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7345 (tpt-90) REVERT: D 442 ASP cc_start: 0.7298 (t0) cc_final: 0.7070 (t0) REVERT: E 142 LYS cc_start: 0.7617 (tttp) cc_final: 0.6908 (tmmt) REVERT: E 234 HIS cc_start: 0.6885 (m90) cc_final: 0.6669 (m90) REVERT: E 254 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8055 (tt) REVERT: F 278 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7009 (tp) REVERT: F 338 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8303 (pttp) REVERT: F 349 THR cc_start: 0.8689 (t) cc_final: 0.8411 (m) REVERT: F 420 ASP cc_start: 0.6441 (p0) cc_final: 0.6016 (p0) outliers start: 86 outliers final: 59 residues processed: 238 average time/residue: 0.5389 time to fit residues: 143.5363 Evaluate side-chains 241 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 165 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 325 GLN Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 338 LYS Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 367 THR Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 187 optimal weight: 0.4980 chunk 201 optimal weight: 8.9990 chunk 93 optimal weight: 0.0470 chunk 172 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.0060 overall best weight: 1.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 HIS D 224 ASN E 233 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.187407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.153528 restraints weight = 18811.488| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.60 r_work: 0.3558 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16983 Z= 0.120 Angle : 0.575 10.995 23087 Z= 0.294 Chirality : 0.045 0.325 2612 Planarity : 0.004 0.050 2974 Dihedral : 9.282 74.880 2533 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 5.14 % Allowed : 36.01 % Favored : 58.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.18), residues: 2117 helix: -1.47 (0.33), residues: 228 sheet: -1.06 (0.22), residues: 487 loop : -0.87 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 412 TYR 0.011 0.001 TYR E 357 PHE 0.022 0.001 PHE F 111 TRP 0.013 0.001 TRP F 406 HIS 0.013 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00280 (16983) covalent geometry : angle 0.57466 (23087) hydrogen bonds : bond 0.02864 ( 194) hydrogen bonds : angle 5.67857 ( 501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4371.46 seconds wall clock time: 75 minutes 24.55 seconds (4524.55 seconds total)