Starting phenix.real_space_refine on Sun May 18 02:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8has_34607/05_2025/8has_34607_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8has_34607/05_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_34607/05_2025/8has_34607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8has_34607/05_2025/8has_34607.map" model { file = "/net/cci-nas-00/data/ceres_data/8has_34607/05_2025/8has_34607_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8has_34607/05_2025/8has_34607_trim.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.18, per 1000 atoms: 0.61 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: 4.38 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.74 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: 3.93 Time building geometry restraints manager: 5.08 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 451 or resid 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: 0.410 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.490 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (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 TRP 0.019 0.001 TRP F 426 HIS 0.020 0.002 HIS F 233 PHE 0.026 0.001 PHE F 111 TYR 0.016 0.001 TYR B 241 ARG 0.006 0.000 ARG C 438 Details of bonding type rmsd hydrogen bonds : bond 0.29874 ( 194) hydrogen bonds : angle 9.52387 ( 501) covalent geometry : bond 0.00866 (16983) covalent geometry : angle 1.22617 (23087) *********************** 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 : 1.827 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: 0.9119 time to fit residues: 318.6645 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 : 1.812 ------------------------------------------------------------------------------- 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 178 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 165 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN C 335 GLN D 233 HIS E 224 ASN 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 = 0.4079 r_free = 0.4079 target = 0.186266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152011 restraints weight = 19057.898| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.64 r_work: 0.3549 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16983 Z= 0.182 Angle : 0.682 11.152 23087 Z= 0.354 Chirality : 0.049 0.302 2612 Planarity : 0.005 0.052 2974 Dihedral : 14.072 87.350 2684 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.00 % Favored : 93.81 % Rotamer: Outliers : 9.55 % Allowed : 32.72 % Favored : 57.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.17), residues: 2117 helix: -2.16 (0.32), residues: 226 sheet: -1.41 (0.22), residues: 480 loop : -1.32 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 406 HIS 0.011 0.002 HIS E 233 PHE 0.027 0.002 PHE D 170 TYR 0.014 0.002 TYR F 241 ARG 0.004 0.001 ARG E 438 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 194) hydrogen bonds : angle 6.62661 ( 501) covalent geometry : bond 0.00427 (16983) covalent geometry : angle 0.68158 (23087) *********************** 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 346 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 175 time to evaluate : 1.879 Fit side-chains REVERT: A 142 LYS cc_start: 0.8329 (pttp) cc_final: 0.7608 (pptt) REVERT: A 240 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6349 (p0) REVERT: A 328 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7665 (tt) REVERT: A 374 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: B 244 GLN cc_start: 0.6862 (mp10) cc_final: 0.6201 (mm110) REVERT: B 254 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 338 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8510 (pttp) REVERT: B 414 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7858 (mtt180) REVERT: C 112 SER cc_start: 0.8787 (p) cc_final: 0.8487 (m) REVERT: C 254 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8184 (tt) REVERT: C 302 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6869 (m-30) REVERT: C 303 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5821 (tt) REVERT: C 438 ARG cc_start: 0.6234 (mpt180) cc_final: 0.6030 (mmt90) REVERT: D 142 LYS cc_start: 0.7643 (ptmm) cc_final: 0.7345 (ptmm) REVERT: D 184 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7160 (mmm) REVERT: D 220 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6484 (mmt90) REVERT: D 224 ASN cc_start: 0.6052 (OUTLIER) cc_final: 0.5846 (p0) REVERT: D 234 HIS cc_start: 0.7604 (m90) cc_final: 0.7284 (m90) REVERT: D 358 ASN cc_start: 0.6005 (OUTLIER) cc_final: 0.5672 (m110) REVERT: D 382 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 442 ASP cc_start: 0.7612 (t0) cc_final: 0.7395 (t0) REVERT: E 142 LYS cc_start: 0.7635 (tttp) cc_final: 0.6903 (tmmt) REVERT: E 234 HIS cc_start: 0.7107 (m90) cc_final: 0.6835 (m90) REVERT: E 328 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7653 (tt) REVERT: E 414 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6915 (mtp85) REVERT: F 89 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7478 (tp40) REVERT: F 98 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7486 (mtp) REVERT: F 241 TYR cc_start: 0.2383 (OUTLIER) cc_final: -0.0136 (m-80) REVERT: F 414 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6391 (mtm180) REVERT: F 415 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8291 (tp) outliers start: 171 outliers final: 96 residues processed: 318 average time/residue: 1.1092 time to fit residues: 397.6984 Evaluate side-chains 265 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 151 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 226 GLN 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 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 374 GLU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 126 LEU 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 239 LEU 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 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 414 ARG 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 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 263 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 303 ILE 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 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 220 ARG 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 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 358 ASN 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 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 315 ASP Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR 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 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 E residue 427 THR Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 199 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 258 VAL 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 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 415 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 9 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 196 optimal weight: 0.0020 chunk 138 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 HIS C 233 HIS C 335 GLN D 233 HIS D 244 GLN E 224 ASN E 233 HIS E 447 ASN F 183 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.149101 restraints weight = 18977.294| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.63 r_work: 0.3509 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16983 Z= 0.174 Angle : 0.655 12.486 23087 Z= 0.338 Chirality : 0.048 0.276 2612 Planarity : 0.004 0.054 2974 Dihedral : 12.678 84.095 2601 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % Rotamer: Outliers : 10.11 % Allowed : 31.43 % Favored : 58.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.17), residues: 2117 helix: -2.16 (0.31), residues: 228 sheet: -1.60 (0.22), residues: 481 loop : -1.35 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 406 HIS 0.011 0.002 HIS A 233 PHE 0.022 0.002 PHE D 170 TYR 0.015 0.001 TYR E 357 ARG 0.006 0.000 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 194) hydrogen bonds : angle 6.33223 ( 501) covalent geometry : bond 0.00411 (16983) covalent geometry : angle 0.65494 (23087) *********************** 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 366 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 185 time to evaluate : 1.816 Fit side-chains REVERT: A 92 ASN cc_start: 0.7226 (p0) cc_final: 0.6970 (t0) REVERT: A 98 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7670 (mtp) REVERT: A 142 LYS cc_start: 0.8192 (pttp) cc_final: 0.7531 (pptt) REVERT: A 234 HIS cc_start: 0.7448 (m90) cc_final: 0.7026 (m90) REVERT: A 240 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6372 (p0) REVERT: A 265 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.5971 (ttt-90) REVERT: A 328 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7748 (tt) REVERT: A 361 LYS cc_start: 0.6588 (mttt) cc_final: 0.6164 (mttm) REVERT: A 374 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: A 382 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8048 (tm-30) REVERT: B 109 ARG cc_start: 0.8040 (ptt180) cc_final: 0.7474 (ptm160) REVERT: B 142 LYS cc_start: 0.7262 (tmmt) cc_final: 0.6978 (tmmt) REVERT: B 217 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8572 (mp) REVERT: B 241 TYR cc_start: 0.5159 (OUTLIER) cc_final: 0.4337 (t80) REVERT: B 244 GLN cc_start: 0.7192 (mp10) cc_final: 0.6572 (mm110) REVERT: B 254 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8082 (tt) REVERT: B 338 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8527 (pttp) REVERT: C 112 SER cc_start: 0.8802 (p) cc_final: 0.8583 (m) REVERT: C 303 ILE cc_start: 0.6137 (OUTLIER) cc_final: 0.5799 (tt) REVERT: C 338 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8071 (pttm) REVERT: C 438 ARG cc_start: 0.6210 (mpt180) cc_final: 0.5987 (mpt180) REVERT: D 142 LYS cc_start: 0.7611 (ptmm) cc_final: 0.7322 (pptt) REVERT: D 377 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: D 382 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7719 (tm-30) REVERT: D 414 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7709 (ttp80) REVERT: E 138 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7846 (ttt-90) REVERT: E 142 LYS cc_start: 0.7662 (tttp) cc_final: 0.6967 (tmmt) REVERT: E 234 HIS cc_start: 0.7380 (m90) cc_final: 0.6858 (m90) REVERT: E 245 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8117 (mtmm) REVERT: E 289 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6290 (ptm160) REVERT: E 328 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7778 (tt) REVERT: E 414 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6963 (mtp85) REVERT: F 98 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7462 (mtp) REVERT: F 230 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7972 (pt) REVERT: F 241 TYR cc_start: 0.1694 (OUTLIER) cc_final: -0.0684 (m-80) REVERT: F 254 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7996 (tt) REVERT: F 338 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8413 (pttp) outliers start: 181 outliers final: 97 residues processed: 340 average time/residue: 1.1690 time to fit residues: 446.2552 Evaluate side-chains 274 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 154 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 235 VAL 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 325 GLN 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 374 GLU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 425 ASN 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 217 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 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 392 THR 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 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 258 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE 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 108 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 219 LYS 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 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 355 LEU 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 404 ILE 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 245 LYS 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 289 ARG 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 325 GLN Chi-restraints excluded: chain E residue 328 LEU 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 123 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 199 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 258 VAL 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 425 ASN 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 49 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 142 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 191 optimal weight: 0.1980 chunk 108 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 HIS C 335 GLN D 233 HIS D 234 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 = 0.4062 r_free = 0.4062 target = 0.185416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151991 restraints weight = 18989.124| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.57 r_work: 0.3540 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16983 Z= 0.128 Angle : 0.594 12.459 23087 Z= 0.306 Chirality : 0.046 0.244 2612 Planarity : 0.004 0.050 2974 Dihedral : 11.645 84.834 2587 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.14 % Rotamer: Outliers : 8.82 % Allowed : 32.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2117 helix: -2.01 (0.32), residues: 228 sheet: -1.32 (0.22), residues: 485 loop : -1.25 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 406 HIS 0.011 0.001 HIS A 233 PHE 0.019 0.001 PHE D 170 TYR 0.012 0.001 TYR E 357 ARG 0.003 0.000 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 194) hydrogen bonds : angle 6.05455 ( 501) covalent geometry : bond 0.00299 (16983) covalent geometry : angle 0.59410 (23087) *********************** 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 338 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 180 time to evaluate : 1.735 Fit side-chains REVERT: A 98 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7744 (mtp) REVERT: A 142 LYS cc_start: 0.8158 (pttp) cc_final: 0.7561 (pptt) REVERT: A 219 LYS cc_start: 0.7150 (ttpp) cc_final: 0.6844 (ttmt) REVERT: A 234 HIS cc_start: 0.7485 (m90) cc_final: 0.7103 (m90) REVERT: A 240 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6100 (p0) REVERT: A 254 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 265 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6034 (ttt-90) REVERT: A 328 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 361 LYS cc_start: 0.6618 (mttt) cc_final: 0.6221 (mttm) REVERT: A 367 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8098 (m) REVERT: A 382 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 109 ARG cc_start: 0.8048 (ptt180) cc_final: 0.7512 (ptm160) REVERT: B 241 TYR cc_start: 0.5062 (OUTLIER) cc_final: 0.4181 (t80) REVERT: B 244 GLN cc_start: 0.7367 (mp10) cc_final: 0.6701 (mm110) REVERT: B 254 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8174 (tt) REVERT: B 338 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8473 (pttp) REVERT: B 414 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7827 (mtt180) REVERT: C 112 SER cc_start: 0.8827 (p) cc_final: 0.8584 (m) REVERT: C 254 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8208 (tt) REVERT: C 303 ILE cc_start: 0.6226 (OUTLIER) cc_final: 0.5917 (tt) REVERT: C 338 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8135 (pttp) REVERT: C 438 ARG cc_start: 0.6032 (mpt180) cc_final: 0.5799 (mpt180) REVERT: D 98 MET cc_start: 0.8010 (mtm) cc_final: 0.7800 (mtp) REVERT: D 142 LYS cc_start: 0.7541 (ptmm) cc_final: 0.7216 (pptt) REVERT: D 230 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7808 (tp) REVERT: D 382 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7860 (tm-30) REVERT: D 414 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7679 (ttp80) REVERT: D 442 ASP cc_start: 0.7354 (t0) cc_final: 0.7070 (t0) REVERT: E 138 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7834 (ttt-90) REVERT: E 142 LYS cc_start: 0.7509 (tttp) cc_final: 0.6888 (tmmt) REVERT: E 234 HIS cc_start: 0.7316 (m90) cc_final: 0.6864 (m90) REVERT: E 254 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7980 (tt) REVERT: E 328 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7794 (tt) REVERT: E 414 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6854 (mtp85) REVERT: E 417 LEU cc_start: 0.4001 (OUTLIER) cc_final: 0.3682 (tt) REVERT: F 98 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7510 (mtp) REVERT: F 230 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8061 (pt) REVERT: F 254 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8092 (tt) REVERT: F 338 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8320 (pttp) outliers start: 158 outliers final: 81 residues processed: 317 average time/residue: 1.1130 time to fit residues: 397.4958 Evaluate side-chains 268 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 163 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 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 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 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 254 LEU Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 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 392 THR Chi-restraints excluded: chain C residue 405 ILE 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 140 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 220 ARG 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 258 VAL Chi-restraints excluded: chain D residue 302 ASP 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 355 LEU 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 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 328 LEU 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 199 ILE Chi-restraints excluded: chain F residue 230 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 121 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 226 GLN B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN E 335 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.182826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148501 restraints weight = 19152.638| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.64 r_work: 0.3499 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16983 Z= 0.164 Angle : 0.626 11.872 23087 Z= 0.323 Chirality : 0.047 0.254 2612 Planarity : 0.004 0.050 2974 Dihedral : 11.655 88.293 2568 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.14 % Favored : 93.72 % Rotamer: Outliers : 10.16 % Allowed : 30.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2117 helix: -2.03 (0.32), residues: 229 sheet: -1.35 (0.22), residues: 477 loop : -1.25 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 406 HIS 0.012 0.002 HIS F 233 PHE 0.021 0.002 PHE D 170 TYR 0.015 0.001 TYR E 357 ARG 0.005 0.000 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 194) hydrogen bonds : angle 6.06156 ( 501) covalent geometry : bond 0.00391 (16983) covalent geometry : angle 0.62618 (23087) *********************** 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 359 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 177 time to evaluate : 1.747 Fit side-chains REVERT: A 98 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7790 (mtp) REVERT: A 142 LYS cc_start: 0.8199 (pttp) cc_final: 0.7638 (pptt) REVERT: A 234 HIS cc_start: 0.7436 (m90) cc_final: 0.7026 (m90) REVERT: A 240 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6129 (p0) REVERT: A 254 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7948 (tt) REVERT: A 265 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.6057 (ttt-90) REVERT: A 328 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7724 (tt) REVERT: B 109 ARG cc_start: 0.8069 (ptt180) cc_final: 0.7655 (ptm160) REVERT: B 142 LYS cc_start: 0.7521 (tmmt) cc_final: 0.6876 (tmmt) REVERT: B 241 TYR cc_start: 0.4877 (OUTLIER) cc_final: 0.3911 (t80) REVERT: B 244 GLN cc_start: 0.7454 (mp10) cc_final: 0.6743 (mm110) REVERT: B 254 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8120 (tt) REVERT: B 338 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8093 (pttp) REVERT: B 414 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7795 (mtt180) REVERT: C 112 SER cc_start: 0.8809 (p) cc_final: 0.8560 (m) REVERT: C 303 ILE cc_start: 0.6260 (OUTLIER) cc_final: 0.5928 (tt) REVERT: C 338 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8035 (pttm) REVERT: C 438 ARG cc_start: 0.6100 (mpt180) cc_final: 0.5841 (mpt180) REVERT: D 142 LYS cc_start: 0.7520 (ptmm) cc_final: 0.7243 (pptt) REVERT: D 184 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7430 (mmm) REVERT: D 270 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7632 (mm) REVERT: D 382 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7854 (tm-30) REVERT: E 138 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7852 (ttt-90) REVERT: E 142 LYS cc_start: 0.7584 (tttp) cc_final: 0.6952 (tmmt) REVERT: E 172 TYR cc_start: 0.6505 (t80) cc_final: 0.6005 (t80) REVERT: E 234 HIS cc_start: 0.7442 (m90) cc_final: 0.6815 (m90) REVERT: E 254 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7998 (tt) REVERT: E 328 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7806 (tt) REVERT: E 414 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6987 (mtp85) REVERT: E 417 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3851 (tt) REVERT: F 98 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7480 (mtp) REVERT: F 230 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8017 (pt) REVERT: F 239 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5633 (tt) REVERT: F 241 TYR cc_start: 0.1339 (OUTLIER) cc_final: -0.0801 (m-80) REVERT: F 254 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8019 (tt) REVERT: F 278 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7118 (tp) REVERT: F 338 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8378 (pttp) outliers start: 182 outliers final: 108 residues processed: 329 average time/residue: 1.1146 time to fit residues: 412.1747 Evaluate side-chains 304 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 171 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 123 LYS 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 235 VAL 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 304 SER 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 414 ARG Chi-restraints excluded: chain A residue 425 ASN 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 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 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 258 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 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 392 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 445 ILE 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 171 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 219 LYS 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 270 ILE Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 308 THR 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 355 LEU 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 404 ILE 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 319 VAL Chi-restraints excluded: chain E residue 324 LEU 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 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 123 LYS Chi-restraints excluded: chain F residue 199 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 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 425 ASN 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 54 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 226 GLN B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 GLN E 335 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148279 restraints weight = 19022.952| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.60 r_work: 0.3498 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16983 Z= 0.192 Angle : 0.664 11.951 23087 Z= 0.341 Chirality : 0.048 0.273 2612 Planarity : 0.004 0.051 2974 Dihedral : 11.897 88.093 2565 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.28 % Favored : 93.58 % Rotamer: Outliers : 10.83 % Allowed : 30.21 % Favored : 58.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 2117 helix: -2.06 (0.31), residues: 230 sheet: -1.37 (0.22), residues: 479 loop : -1.28 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 406 HIS 0.012 0.002 HIS B 233 PHE 0.022 0.002 PHE D 170 TYR 0.017 0.001 TYR E 357 ARG 0.004 0.000 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 194) hydrogen bonds : angle 6.13098 ( 501) covalent geometry : bond 0.00461 (16983) covalent geometry : angle 0.66381 (23087) *********************** 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 371 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 177 time to evaluate : 1.887 Fit side-chains REVERT: A 98 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7790 (mtp) REVERT: A 133 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 142 LYS cc_start: 0.8170 (pttp) cc_final: 0.7665 (pptt) REVERT: A 219 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6855 (ttmm) REVERT: A 234 HIS cc_start: 0.7512 (m90) cc_final: 0.7122 (m90) REVERT: A 240 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6146 (p0) REVERT: A 265 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6125 (ttt-90) REVERT: A 328 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 361 LYS cc_start: 0.6687 (mttt) cc_final: 0.6227 (mttm) REVERT: A 367 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8097 (m) REVERT: B 109 ARG cc_start: 0.8340 (ptt180) cc_final: 0.7806 (ptm160) REVERT: B 142 LYS cc_start: 0.7416 (tmmt) cc_final: 0.6763 (tmmt) REVERT: B 204 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.7650 (tt0) REVERT: B 219 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6931 (mtmm) REVERT: B 234 HIS cc_start: 0.7299 (m90) cc_final: 0.7053 (m90) REVERT: B 241 TYR cc_start: 0.4909 (OUTLIER) cc_final: 0.3970 (t80) REVERT: B 244 GLN cc_start: 0.7552 (mp10) cc_final: 0.6837 (mm110) REVERT: B 254 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8052 (tt) REVERT: B 338 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8120 (pttp) REVERT: B 414 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7775 (mtt180) REVERT: C 112 SER cc_start: 0.8825 (p) cc_final: 0.8546 (m) REVERT: C 254 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8127 (tt) REVERT: C 303 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5792 (tt) REVERT: C 338 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8044 (pttm) REVERT: C 438 ARG cc_start: 0.6157 (mpt180) cc_final: 0.5931 (mpt180) REVERT: D 142 LYS cc_start: 0.7547 (ptmm) cc_final: 0.7218 (pptt) REVERT: D 184 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7324 (mmm) REVERT: D 230 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7873 (tp) REVERT: D 234 HIS cc_start: 0.7499 (m90) cc_final: 0.7049 (m90) REVERT: D 338 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8360 (pttp) REVERT: D 382 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 138 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7871 (ttt-90) REVERT: E 142 LYS cc_start: 0.7601 (tttp) cc_final: 0.6957 (tmmt) REVERT: E 234 HIS cc_start: 0.7518 (m90) cc_final: 0.6950 (m90) REVERT: E 289 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5755 (ptm160) REVERT: E 328 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7881 (tt) REVERT: E 414 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7126 (mtp85) REVERT: E 417 LEU cc_start: 0.4018 (OUTLIER) cc_final: 0.3778 (tt) REVERT: F 98 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7570 (mtp) REVERT: F 230 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8008 (pt) REVERT: F 241 TYR cc_start: 0.1243 (OUTLIER) cc_final: -0.0645 (m-80) REVERT: F 254 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8027 (tt) REVERT: F 338 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8559 (pttp) outliers start: 194 outliers final: 114 residues processed: 344 average time/residue: 1.0975 time to fit residues: 425.5698 Evaluate side-chains 310 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 168 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 133 LEU 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 235 VAL 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 304 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 GLN 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 414 ARG Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 98 MET 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 219 LYS 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 392 THR Chi-restraints excluded: chain B residue 393 SER 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 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 237 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 341 ARG 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 405 ILE 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 140 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 222 THR 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 258 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 338 LYS 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 355 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 387 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 105 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 273 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 289 ARG 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 349 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 123 LYS Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 199 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 258 VAL 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 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 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 450 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 179 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 202 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.148427 restraints weight = 18921.313| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.59 r_work: 0.3500 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16983 Z= 0.183 Angle : 0.656 11.812 23087 Z= 0.337 Chirality : 0.048 0.280 2612 Planarity : 0.004 0.050 2974 Dihedral : 11.779 76.220 2565 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.09 % Favored : 93.76 % Rotamer: Outliers : 10.27 % Allowed : 30.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.17), residues: 2117 helix: -2.00 (0.31), residues: 229 sheet: -1.31 (0.22), residues: 481 loop : -1.27 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 406 HIS 0.013 0.002 HIS B 233 PHE 0.021 0.002 PHE B 269 TYR 0.018 0.001 TYR E 357 ARG 0.004 0.000 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 194) hydrogen bonds : angle 6.05878 ( 501) covalent geometry : bond 0.00439 (16983) covalent geometry : angle 0.65594 (23087) *********************** 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 362 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 178 time to evaluate : 1.786 Fit side-chains REVERT: A 92 ASN cc_start: 0.7212 (p0) cc_final: 0.6996 (t0) REVERT: A 98 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7758 (mtp) REVERT: A 133 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8256 (mt) REVERT: A 142 LYS cc_start: 0.8192 (pttp) cc_final: 0.7642 (pptt) REVERT: A 172 TYR cc_start: 0.4641 (OUTLIER) cc_final: 0.4210 (m-80) REVERT: A 219 LYS cc_start: 0.7183 (ttpp) cc_final: 0.6864 (ttmm) REVERT: A 234 HIS cc_start: 0.7525 (m90) cc_final: 0.7148 (m90) REVERT: A 240 ASP cc_start: 0.6644 (m-30) cc_final: 0.6230 (p0) REVERT: A 241 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.4447 (t80) REVERT: A 254 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.7991 (tt) REVERT: A 265 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6165 (ttt-90) REVERT: A 328 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7817 (tt) REVERT: A 361 LYS cc_start: 0.6673 (mttt) cc_final: 0.6303 (mttm) REVERT: A 367 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8093 (m) REVERT: A 414 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6207 (ptm-80) REVERT: B 109 ARG cc_start: 0.8414 (ptt180) cc_final: 0.7895 (ptm160) REVERT: B 142 LYS cc_start: 0.7637 (tmmt) cc_final: 0.7054 (tmmt) REVERT: B 204 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: B 219 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.7003 (ptpt) REVERT: B 234 HIS cc_start: 0.7328 (m90) cc_final: 0.7109 (m90) REVERT: B 241 TYR cc_start: 0.4742 (OUTLIER) cc_final: 0.3824 (t80) REVERT: B 244 GLN cc_start: 0.7657 (mp10) cc_final: 0.6904 (mm110) REVERT: B 254 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8091 (tt) REVERT: B 338 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8447 (pttm) REVERT: B 414 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7800 (mtt180) REVERT: C 112 SER cc_start: 0.8830 (p) cc_final: 0.8516 (m) REVERT: C 142 LYS cc_start: 0.7676 (pptt) cc_final: 0.7338 (tttp) REVERT: C 219 LYS cc_start: 0.7168 (ttpp) cc_final: 0.6834 (ttmm) REVERT: C 254 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8122 (tt) REVERT: C 303 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5837 (tt) REVERT: C 328 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7870 (tt) REVERT: C 338 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7988 (pttp) REVERT: C 438 ARG cc_start: 0.6113 (mpt180) cc_final: 0.5861 (mpt180) REVERT: D 142 LYS cc_start: 0.7511 (ptmm) cc_final: 0.7235 (pptt) REVERT: D 184 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7336 (mmm) REVERT: D 230 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7820 (tp) REVERT: D 234 HIS cc_start: 0.7441 (m90) cc_final: 0.7000 (m90) REVERT: D 338 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8353 (pttp) REVERT: D 382 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7753 (tm-30) REVERT: D 431 ASP cc_start: 0.8562 (m-30) cc_final: 0.8334 (m-30) REVERT: E 138 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7869 (ttt-90) REVERT: E 142 LYS cc_start: 0.7656 (tttp) cc_final: 0.6945 (tmmt) REVERT: E 234 HIS cc_start: 0.7552 (m90) cc_final: 0.6958 (m90) REVERT: E 328 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7894 (tt) REVERT: E 382 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: E 414 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7177 (mtp85) REVERT: F 98 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7554 (mtp) REVERT: F 230 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7991 (pt) REVERT: F 241 TYR cc_start: 0.1408 (OUTLIER) cc_final: -0.0728 (m-80) REVERT: F 254 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8004 (tt) REVERT: F 338 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8556 (pttp) outliers start: 184 outliers final: 113 residues processed: 338 average time/residue: 1.0797 time to fit residues: 411.8553 Evaluate side-chains 313 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 169 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 TYR 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 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 304 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 GLN 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 414 ARG Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 98 MET 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 219 LYS 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 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 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 258 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 341 ARG 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 405 ILE 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 171 SER Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 222 THR 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 258 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 338 LYS 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 355 LEU 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 387 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 404 ILE 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 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 349 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 382 GLU 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 126 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 199 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 258 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS C 335 GLN C 421 HIS D 233 HIS D 411 ASN E 335 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148133 restraints weight = 18916.139| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.58 r_work: 0.3497 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16983 Z= 0.187 Angle : 0.660 11.880 23087 Z= 0.338 Chirality : 0.048 0.291 2612 Planarity : 0.004 0.050 2974 Dihedral : 11.641 75.695 2558 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.28 % Favored : 93.58 % Rotamer: Outliers : 9.66 % Allowed : 31.71 % Favored : 58.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.17), residues: 2117 helix: -1.98 (0.31), residues: 229 sheet: -1.38 (0.22), residues: 493 loop : -1.27 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 406 HIS 0.012 0.002 HIS A 233 PHE 0.022 0.002 PHE B 269 TYR 0.015 0.001 TYR F 241 ARG 0.004 0.000 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 194) hydrogen bonds : angle 6.10125 ( 501) covalent geometry : bond 0.00449 (16983) covalent geometry : angle 0.66021 (23087) *********************** 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 355 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 182 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7219 (p0) cc_final: 0.7005 (t0) REVERT: A 98 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7721 (mtp) REVERT: A 133 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 142 LYS cc_start: 0.8167 (pttp) cc_final: 0.7649 (pptt) REVERT: A 172 TYR cc_start: 0.4677 (OUTLIER) cc_final: 0.4074 (m-80) REVERT: A 219 LYS cc_start: 0.7183 (ttpp) cc_final: 0.6861 (ttmm) REVERT: A 234 HIS cc_start: 0.7520 (m90) cc_final: 0.7131 (m90) REVERT: A 240 ASP cc_start: 0.6484 (m-30) cc_final: 0.6174 (p0) REVERT: A 241 TYR cc_start: 0.5646 (OUTLIER) cc_final: 0.5361 (m-80) REVERT: A 254 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 265 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6158 (ttt-90) REVERT: A 328 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7817 (tt) REVERT: A 367 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8171 (m) REVERT: A 414 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6229 (ptm-80) REVERT: A 438 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6351 (tpp-160) REVERT: B 109 ARG cc_start: 0.8434 (ptt180) cc_final: 0.7916 (ptm160) REVERT: B 142 LYS cc_start: 0.7535 (tmmt) cc_final: 0.6927 (tmmt) REVERT: B 204 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: B 219 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.7001 (ptpt) REVERT: B 234 HIS cc_start: 0.7354 (m90) cc_final: 0.7134 (m90) REVERT: B 241 TYR cc_start: 0.4824 (OUTLIER) cc_final: 0.3880 (t80) REVERT: B 244 GLN cc_start: 0.7606 (mp10) cc_final: 0.6817 (mm110) REVERT: B 254 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8064 (tt) REVERT: B 338 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8450 (pttm) REVERT: B 414 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7773 (mtt180) REVERT: C 112 SER cc_start: 0.8840 (p) cc_final: 0.8522 (m) REVERT: C 142 LYS cc_start: 0.7628 (pptt) cc_final: 0.7302 (tttp) REVERT: C 219 LYS cc_start: 0.7116 (ttpp) cc_final: 0.6806 (ttmm) REVERT: C 254 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8115 (tt) REVERT: C 303 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5735 (tt) REVERT: C 328 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8035 (tt) REVERT: C 338 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7998 (pttp) REVERT: C 417 LEU cc_start: 0.4182 (OUTLIER) cc_final: 0.3901 (mp) REVERT: C 438 ARG cc_start: 0.6142 (mpt180) cc_final: 0.5888 (mpt180) REVERT: D 142 LYS cc_start: 0.7548 (ptmm) cc_final: 0.7222 (pptt) REVERT: D 184 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7331 (mmm) REVERT: D 230 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7828 (tp) REVERT: D 234 HIS cc_start: 0.7402 (m90) cc_final: 0.6953 (m90) REVERT: D 270 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7834 (mm) REVERT: D 338 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8357 (pttp) REVERT: D 442 ASP cc_start: 0.7483 (t0) cc_final: 0.7253 (t0) REVERT: E 92 ASN cc_start: 0.7164 (p0) cc_final: 0.6912 (t0) REVERT: E 138 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7872 (ttt-90) REVERT: E 142 LYS cc_start: 0.7663 (tttp) cc_final: 0.6927 (tmmt) REVERT: E 234 HIS cc_start: 0.7489 (m90) cc_final: 0.6933 (m90) REVERT: E 328 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7883 (tt) REVERT: E 382 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: E 414 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7198 (mtp85) REVERT: F 98 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7590 (mtp) REVERT: F 230 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7989 (pt) REVERT: F 239 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5758 (tt) REVERT: F 241 TYR cc_start: 0.1249 (OUTLIER) cc_final: -0.0689 (m-80) REVERT: F 254 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8003 (tt) outliers start: 173 outliers final: 114 residues processed: 331 average time/residue: 1.1163 time to fit residues: 416.8283 Evaluate side-chains 317 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 169 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 TYR 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 304 SER Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 GLN 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 414 ARG Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 438 ARG 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 219 LYS 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 267 THR 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 392 THR 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 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 258 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 341 ARG 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 405 ILE 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 173 TYR Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 219 LYS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 222 THR 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 258 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 338 LYS 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 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 387 SER Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 404 ILE 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 105 SER Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 156 GLU 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 349 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 382 GLU 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 126 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 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 258 VAL Chi-restraints excluded: chain F residue 271 THR 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 325 GLN Chi-restraints excluded: chain F residue 328 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 112 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 144 optimal weight: 0.0030 chunk 204 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS C 335 GLN C 421 HIS D 233 HIS E 335 GLN 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 = 0.186983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.153685 restraints weight = 19013.658| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.53 r_work: 0.3566 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16983 Z= 0.106 Angle : 0.568 11.211 23087 Z= 0.293 Chirality : 0.045 0.265 2612 Planarity : 0.004 0.049 2974 Dihedral : 10.395 75.093 2556 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.38 % Rotamer: Outliers : 6.20 % Allowed : 35.23 % Favored : 58.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.18), residues: 2117 helix: -1.58 (0.33), residues: 227 sheet: -1.22 (0.21), residues: 516 loop : -1.07 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 406 HIS 0.012 0.001 HIS E 233 PHE 0.022 0.001 PHE B 269 TYR 0.009 0.001 TYR C 259 ARG 0.003 0.000 ARG E 289 Details of bonding type rmsd hydrogen bonds : bond 0.02807 ( 194) hydrogen bonds : angle 5.74216 ( 501) covalent geometry : bond 0.00240 (16983) covalent geometry : angle 0.56807 (23087) *********************** 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 296 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 185 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7792 (mtp) REVERT: A 142 LYS cc_start: 0.8129 (pttp) cc_final: 0.7633 (pptt) REVERT: A 172 TYR cc_start: 0.4425 (OUTLIER) cc_final: 0.3939 (m-80) REVERT: A 219 LYS cc_start: 0.7028 (ttpp) cc_final: 0.6796 (ttmt) REVERT: A 234 HIS cc_start: 0.7312 (m90) cc_final: 0.6918 (m90) REVERT: A 241 TYR cc_start: 0.5623 (OUTLIER) cc_final: 0.4335 (t80) REVERT: A 245 LYS cc_start: 0.8664 (mttp) cc_final: 0.8427 (mmtp) REVERT: A 254 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8075 (tt) REVERT: A 265 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6069 (ttt-90) REVERT: B 89 GLN cc_start: 0.7464 (tp40) cc_final: 0.5923 (tm-30) REVERT: B 109 ARG cc_start: 0.8396 (ptt180) cc_final: 0.7880 (ptm160) REVERT: B 110 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7733 (mtt180) REVERT: B 142 LYS cc_start: 0.7608 (tmmt) cc_final: 0.7029 (tmmt) REVERT: B 234 HIS cc_start: 0.7265 (m90) cc_final: 0.7062 (m90) REVERT: B 241 TYR cc_start: 0.4661 (OUTLIER) cc_final: 0.3764 (t80) REVERT: B 244 GLN cc_start: 0.7458 (mp10) cc_final: 0.6842 (mm-40) REVERT: B 254 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 414 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7794 (mtt180) REVERT: C 112 SER cc_start: 0.8821 (p) cc_final: 0.8526 (m) REVERT: C 254 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8211 (tt) REVERT: C 303 ILE cc_start: 0.5992 (OUTLIER) cc_final: 0.5765 (tt) REVERT: C 328 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8103 (tt) REVERT: C 338 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7833 (pttm) REVERT: C 438 ARG cc_start: 0.6041 (OUTLIER) cc_final: 0.5824 (mpt180) REVERT: D 142 LYS cc_start: 0.7457 (ptmm) cc_final: 0.7238 (pptt) REVERT: D 234 HIS cc_start: 0.7349 (m90) cc_final: 0.6959 (m90) REVERT: D 254 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8132 (tt) REVERT: D 270 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7815 (mm) REVERT: D 382 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 442 ASP cc_start: 0.7298 (t0) cc_final: 0.7084 (t0) REVERT: E 138 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7877 (ttt-90) REVERT: E 142 LYS cc_start: 0.7593 (tttp) cc_final: 0.6993 (tmmt) REVERT: E 254 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8058 (tt) REVERT: E 328 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7813 (tt) REVERT: F 98 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7545 (mtp) REVERT: F 254 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8070 (tt) REVERT: F 349 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8416 (m) REVERT: F 420 ASP cc_start: 0.6415 (p0) cc_final: 0.6005 (p0) outliers start: 111 outliers final: 64 residues processed: 277 average time/residue: 1.1834 time to fit residues: 367.8454 Evaluate side-chains 256 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 171 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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 315 ASP Chi-restraints excluded: chain A residue 325 GLN 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 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 267 THR 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 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 237 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE 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 424 GLU Chi-restraints excluded: chain C residue 438 ARG 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 173 TYR 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 270 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 308 THR 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 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 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 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 129 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 254 LEU 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 418 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 185 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS C 183 GLN C 335 GLN D 233 HIS E 204 GLN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.178997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144393 restraints weight = 19022.107| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.58 r_work: 0.3451 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 16983 Z= 0.311 Angle : 0.784 12.324 23087 Z= 0.402 Chirality : 0.054 0.412 2612 Planarity : 0.005 0.049 2974 Dihedral : 12.292 80.688 2545 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.46 % Favored : 92.39 % Rotamer: Outliers : 6.42 % Allowed : 35.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2117 helix: -2.19 (0.30), residues: 232 sheet: -1.28 (0.23), residues: 462 loop : -1.34 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP F 406 HIS 0.015 0.002 HIS C 233 PHE 0.025 0.003 PHE D 170 TYR 0.025 0.002 TYR F 241 ARG 0.005 0.001 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.04987 ( 194) hydrogen bonds : angle 6.39214 ( 501) covalent geometry : bond 0.00756 (16983) covalent geometry : angle 0.78404 (23087) ********************** 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 270 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 155 time to evaluate : 1.744 Fit side-chains REVERT: A 92 ASN cc_start: 0.7234 (p0) cc_final: 0.7007 (t0) REVERT: A 98 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: A 142 LYS cc_start: 0.8243 (pttp) cc_final: 0.7629 (pptt) REVERT: A 172 TYR cc_start: 0.4799 (OUTLIER) cc_final: 0.4117 (m-80) REVERT: A 234 HIS cc_start: 0.7721 (m90) cc_final: 0.7341 (m90) REVERT: A 240 ASP cc_start: 0.6551 (m-30) cc_final: 0.6213 (p0) REVERT: A 245 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8482 (mmtp) REVERT: A 265 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6423 (ttt-90) REVERT: A 367 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8194 (m) REVERT: A 414 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6332 (ptm-80) REVERT: B 109 ARG cc_start: 0.8496 (ptt180) cc_final: 0.7949 (ptm160) REVERT: B 142 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7149 (tmmt) REVERT: B 204 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: B 234 HIS cc_start: 0.7400 (m90) cc_final: 0.7136 (m90) REVERT: B 241 TYR cc_start: 0.4947 (OUTLIER) cc_final: 0.3938 (t80) REVERT: B 244 GLN cc_start: 0.7576 (mp10) cc_final: 0.6810 (mm110) REVERT: C 112 SER cc_start: 0.8852 (p) cc_final: 0.8502 (m) REVERT: C 303 ILE cc_start: 0.6033 (OUTLIER) cc_final: 0.5727 (tt) REVERT: C 328 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8002 (tt) REVERT: C 438 ARG cc_start: 0.6177 (mpt180) cc_final: 0.5873 (mpt180) REVERT: D 142 LYS cc_start: 0.7606 (ptmm) cc_final: 0.7281 (pptt) REVERT: D 234 HIS cc_start: 0.7585 (m90) cc_final: 0.7039 (m90) REVERT: D 246 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8591 (mmt) REVERT: D 382 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7543 (tm-30) REVERT: E 92 ASN cc_start: 0.7141 (p0) cc_final: 0.6919 (t0) REVERT: E 138 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7889 (ttt-90) REVERT: E 142 LYS cc_start: 0.7692 (tttp) cc_final: 0.6970 (tmmt) REVERT: E 234 HIS cc_start: 0.7548 (m90) cc_final: 0.7002 (m90) REVERT: E 289 ARG cc_start: 0.7444 (ptp90) cc_final: 0.7129 (ptt180) REVERT: E 328 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7912 (tt) REVERT: F 98 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7625 (mtp) outliers start: 115 outliers final: 78 residues processed: 255 average time/residue: 1.0773 time to fit residues: 310.6410 Evaluate side-chains 243 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 151 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 245 LYS Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 346 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 454 VAL 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 267 THR 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 328 LEU 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 392 THR 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 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 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR 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 173 TYR 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 246 MET 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 308 THR 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 357 TYR Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL 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 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 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 199 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 271 THR 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 326 CYS 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 443 ILE 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 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 141 optimal weight: 0.0020 chunk 159 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 HIS B 421 HIS D 233 HIS E 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154416 restraints weight = 18961.721| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.60 r_work: 0.3570 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16983 Z= 0.100 Angle : 0.571 11.062 23087 Z= 0.296 Chirality : 0.045 0.278 2612 Planarity : 0.004 0.048 2974 Dihedral : 10.235 74.571 2545 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 4.52 % Allowed : 37.24 % Favored : 58.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 2117 helix: -1.58 (0.33), residues: 228 sheet: -1.16 (0.22), residues: 494 loop : -1.04 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 406 HIS 0.013 0.001 HIS E 233 PHE 0.022 0.001 PHE B 269 TYR 0.009 0.001 TYR E 259 ARG 0.004 0.000 ARG A 438 Details of bonding type rmsd hydrogen bonds : bond 0.02644 ( 194) hydrogen bonds : angle 5.75070 ( 501) covalent geometry : bond 0.00222 (16983) covalent geometry : angle 0.57090 (23087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9810.93 seconds wall clock time: 169 minutes 49.18 seconds (10189.18 seconds total)