Starting phenix.real_space_refine on Sat Jun 14 18:34:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8has_34607/06_2025/8has_34607_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8has_34607/06_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_34607/06_2025/8has_34607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8has_34607/06_2025/8has_34607.map" model { file = "/net/cci-nas-00/data/ceres_data/8has_34607/06_2025/8has_34607_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8has_34607/06_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-5710/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: 10.26, per 1000 atoms: 0.62 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: 3.63 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: 1.67 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: 4.33 Time building geometry restraints manager: 4.48 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.760 Find NCS groups from input model: 1.220 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: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.730 ------------------------------------------------------------------------------- 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 : 1.715 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: 0.9116 time to fit residues: 318.3819 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 : 1.946 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152012 restraints weight = 19057.895| |-----------------------------------------------------------------------------| 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 : 1.742 Fit side-chains REVERT: A 142 LYS cc_start: 0.8329 (pttp) cc_final: 0.7609 (pptt) REVERT: A 240 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6351 (p0) REVERT: A 328 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7666 (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: 0.8051 (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: 0.6870 (m-30) REVERT: C 303 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5822 (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: 0.7161 (mmm) REVERT: D 220 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6485 (mmt90) REVERT: D 224 ASN cc_start: 0.6052 (OUTLIER) cc_final: 0.5847 (p0) REVERT: D 234 HIS cc_start: 0.7604 (m90) cc_final: 0.7285 (m90) REVERT: D 358 ASN cc_start: 0.6006 (OUTLIER) cc_final: 0.5673 (m110) REVERT: D 382 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 442 ASP cc_start: 0.7611 (t0) cc_final: 0.7394 (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: 0.6836 (m90) REVERT: E 328 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7654 (tt) REVERT: E 414 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6915 (mtp85) REVERT: F 89 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7477 (tp40) REVERT: F 98 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7486 (mtp) REVERT: F 241 TYR cc_start: 0.2385 (OUTLIER) cc_final: -0.0135 (m-80) REVERT: F 414 ARG cc_start: 0.7016 (mtt90) cc_final: 0.6391 (mtm180) REVERT: F 415 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8292 (tp) outliers start: 171 outliers final: 96 residues processed: 318 average time/residue: 1.1433 time to fit residues: 408.5974 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 : 1.774 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 6.9990 chunk 103 optimal weight: 0.0870 chunk 196 optimal weight: 3.9990 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: 0.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 F 183 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.183460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149489 restraints weight = 18984.042| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.63 r_work: 0.3511 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2274 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= 0.171 Angle : 0.646 12.101 23087 Z= 0.334 Chirality : 0.048 0.267 2612 Planarity : 0.004 0.053 2974 Dihedral : 12.717 85.532 2601 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.00 % Favored : 93.81 % Rotamer: Outliers : 9.66 % Allowed : 32.10 % 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: -2.23 (0.17), residues: 2117 helix: -2.15 (0.31), residues: 228 sheet: -1.63 (0.22), residues: 476 loop : -1.33 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 406 HIS 0.011 0.001 HIS D 233 PHE 0.022 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 0.04176 ( 194) hydrogen bonds : angle 6.33510 ( 501) covalent geometry : bond 0.00402 (16983) covalent geometry : angle 0.64587 (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 353 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 180 time to evaluate : 1.686 Fit side-chains REVERT: A 98 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7408 (mtp) REVERT: A 142 LYS cc_start: 0.8216 (pttp) cc_final: 0.7573 (pptt) REVERT: A 234 HIS cc_start: 0.7450 (m90) cc_final: 0.7019 (m90) REVERT: A 240 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.6325 (p0) REVERT: A 265 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5960 (ttt-90) REVERT: A 328 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7721 (tt) REVERT: A 361 LYS cc_start: 0.6584 (mttt) cc_final: 0.6162 (mttm) REVERT: A 374 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: B 109 ARG cc_start: 0.8041 (ptt180) cc_final: 0.7480 (ptm160) REVERT: B 217 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 241 TYR cc_start: 0.5241 (OUTLIER) cc_final: 0.4275 (t80) REVERT: B 244 GLN cc_start: 0.7225 (mp10) cc_final: 0.6531 (mm110) REVERT: B 254 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8099 (tt) REVERT: B 338 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8523 (pttp) REVERT: C 112 SER cc_start: 0.8816 (p) cc_final: 0.8574 (m) REVERT: C 302 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: C 303 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5792 (tt) REVERT: C 338 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8217 (pttm) REVERT: C 438 ARG cc_start: 0.6336 (mpt180) cc_final: 0.6126 (mpt180) REVERT: D 142 LYS cc_start: 0.7584 (ptmm) cc_final: 0.7286 (pptt) REVERT: D 230 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7992 (tp) REVERT: D 338 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8409 (pttp) REVERT: D 382 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7802 (tm-30) REVERT: D 414 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7726 (ttp80) REVERT: E 138 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7831 (ttt-90) REVERT: E 142 LYS cc_start: 0.7618 (tttp) cc_final: 0.6937 (tmmt) REVERT: E 234 HIS cc_start: 0.7454 (m90) cc_final: 0.6950 (m90) REVERT: E 245 LYS cc_start: 0.8331 (mttp) cc_final: 0.8090 (mtmm) REVERT: E 328 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7754 (tt) REVERT: E 367 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8362 (m) REVERT: E 414 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6934 (mtp85) REVERT: F 98 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7515 (mtp) REVERT: F 241 TYR cc_start: 0.1863 (OUTLIER) cc_final: -0.0639 (m-80) REVERT: F 254 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8013 (tt) REVERT: F 338 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8385 (pttp) outliers start: 173 outliers final: 96 residues processed: 330 average time/residue: 1.1943 time to fit residues: 441.5519 Evaluate side-chains 271 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 152 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 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 263 VAL 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 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 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 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 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 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 315 ASP Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 367 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 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: 7.9990 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 186 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 226 GLN E 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.181266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146970 restraints weight = 18992.438| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.62 r_work: 0.3481 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16983 Z= 0.207 Angle : 0.693 12.754 23087 Z= 0.356 Chirality : 0.049 0.253 2612 Planarity : 0.005 0.053 2974 Dihedral : 12.692 84.092 2591 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 10.11 % Allowed : 31.21 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (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: -2.27 (0.17), residues: 2117 helix: -2.23 (0.31), residues: 230 sheet: -1.51 (0.22), residues: 489 loop : -1.40 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 406 HIS 0.011 0.002 HIS F 233 PHE 0.024 0.002 PHE D 170 TYR 0.017 0.002 TYR E 357 ARG 0.005 0.001 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 194) hydrogen bonds : angle 6.35594 ( 501) covalent geometry : bond 0.00495 (16983) covalent geometry : angle 0.69278 (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 351 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 170 time to evaluate : 1.678 Fit side-chains REVERT: A 92 ASN cc_start: 0.7205 (p0) cc_final: 0.6995 (t0) REVERT: A 98 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7692 (mtp) REVERT: A 142 LYS cc_start: 0.8146 (pttp) cc_final: 0.7511 (pptt) REVERT: A 234 HIS cc_start: 0.7457 (m90) cc_final: 0.7014 (m90) REVERT: A 240 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6249 (p0) REVERT: A 265 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.6080 (ttt-90) REVERT: A 328 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 367 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8094 (m) REVERT: A 374 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: B 109 ARG cc_start: 0.8089 (ptt180) cc_final: 0.7568 (ptm160) REVERT: B 142 LYS cc_start: 0.7321 (tmmt) cc_final: 0.6730 (tmmt) REVERT: B 217 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 241 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.4042 (t80) REVERT: B 244 GLN cc_start: 0.7492 (mp10) cc_final: 0.6731 (mm110) REVERT: B 338 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8132 (pttp) REVERT: B 414 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7778 (mtt180) REVERT: C 112 SER cc_start: 0.8812 (p) cc_final: 0.8536 (m) REVERT: C 237 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7010 (t) REVERT: C 303 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5872 (tt) REVERT: C 338 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7944 (pttp) REVERT: C 438 ARG cc_start: 0.6163 (mpt180) cc_final: 0.5912 (mpt180) REVERT: D 142 LYS cc_start: 0.7625 (ptmm) cc_final: 0.7291 (pptt) REVERT: D 184 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7436 (mmm) REVERT: D 270 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7615 (mm) REVERT: D 382 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 414 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7692 (ttp80) REVERT: E 138 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7914 (ttt-90) REVERT: E 142 LYS cc_start: 0.7609 (tttp) cc_final: 0.6932 (tmmt) REVERT: E 172 TYR cc_start: 0.6576 (t80) cc_final: 0.6304 (t80) REVERT: E 234 HIS cc_start: 0.7469 (m90) cc_final: 0.6871 (m90) REVERT: E 245 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: E 289 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.6197 (ptm160) REVERT: E 328 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7877 (tt) REVERT: E 367 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8362 (m) REVERT: E 414 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7011 (mtp85) REVERT: E 417 LEU cc_start: 0.4127 (OUTLIER) cc_final: 0.3714 (tt) REVERT: F 98 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7530 (mtp) REVERT: F 156 GLU cc_start: 0.7023 (tp30) cc_final: 0.6101 (mp0) REVERT: F 241 TYR cc_start: 0.1305 (OUTLIER) cc_final: -0.0870 (m-80) REVERT: F 338 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8414 (pttp) outliers start: 181 outliers final: 108 residues processed: 330 average time/residue: 1.3537 time to fit residues: 506.2973 Evaluate side-chains 289 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 155 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 107 ILE 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 374 GLU Chi-restraints excluded: chain A residue 418 THR 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 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 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 394 GLN Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 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 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 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 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 271 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 325 GLN 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 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 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 315 ASP Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 367 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 F residue 98 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 121 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 226 GLN B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152962 restraints weight = 19175.672| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.63 r_work: 0.3550 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16983 Z= 0.112 Angle : 0.572 11.895 23087 Z= 0.296 Chirality : 0.045 0.244 2612 Planarity : 0.004 0.050 2974 Dihedral : 11.311 86.466 2581 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.62 % Favored : 94.24 % Rotamer: Outliers : 8.77 % Allowed : 32.05 % Favored : 59.18 % 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: -1.98 (0.18), residues: 2117 helix: -1.93 (0.32), residues: 227 sheet: -1.34 (0.22), residues: 499 loop : -1.20 (0.16), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 275 HIS 0.011 0.001 HIS D 233 PHE 0.018 0.001 PHE B 269 TYR 0.012 0.001 TYR E 357 ARG 0.009 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 194) hydrogen bonds : angle 5.94146 ( 501) covalent geometry : bond 0.00255 (16983) covalent geometry : angle 0.57172 (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 347 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 190 time to evaluate : 2.427 Fit side-chains REVERT: A 98 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7712 (mtp) REVERT: A 142 LYS cc_start: 0.8135 (pttp) cc_final: 0.7580 (pptt) REVERT: A 219 LYS cc_start: 0.7001 (ttpp) cc_final: 0.6704 (ttmt) REVERT: A 234 HIS cc_start: 0.7433 (m90) cc_final: 0.7015 (m90) REVERT: A 240 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6113 (p0) REVERT: A 254 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8087 (tt) REVERT: A 265 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6027 (ttt-90) REVERT: A 328 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7723 (tt) REVERT: A 374 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: A 431 ASP cc_start: 0.8542 (m-30) cc_final: 0.8315 (m-30) REVERT: B 109 ARG cc_start: 0.8027 (ptt180) cc_final: 0.7631 (ptm160) REVERT: B 142 LYS cc_start: 0.7392 (tmmt) cc_final: 0.6767 (tmmt) REVERT: B 219 LYS cc_start: 0.7252 (mtmm) cc_final: 0.6995 (ptpt) REVERT: B 241 TYR cc_start: 0.4664 (OUTLIER) cc_final: 0.3800 (t80) REVERT: B 244 GLN cc_start: 0.7345 (mp10) cc_final: 0.6668 (mm110) REVERT: B 254 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8191 (tt) REVERT: B 414 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7831 (mtt180) REVERT: C 112 SER cc_start: 0.8812 (p) cc_final: 0.8535 (m) REVERT: C 254 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8236 (tt) REVERT: C 303 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5853 (tt) REVERT: C 335 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: C 338 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8062 (pttm) REVERT: C 438 ARG cc_start: 0.6122 (mpt180) cc_final: 0.5847 (mpt180) REVERT: D 98 MET cc_start: 0.7816 (mtp) cc_final: 0.7585 (mtt) REVERT: D 142 LYS cc_start: 0.7472 (ptmm) cc_final: 0.7204 (pptt) REVERT: D 234 HIS cc_start: 0.7367 (m90) cc_final: 0.6931 (m90) REVERT: D 270 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7534 (mm) REVERT: D 382 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7815 (tm-30) REVERT: E 138 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7831 (ttt-90) REVERT: E 142 LYS cc_start: 0.7604 (tttp) cc_final: 0.6948 (tmmt) REVERT: E 234 HIS cc_start: 0.7386 (m90) cc_final: 0.6789 (m90) REVERT: E 254 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8044 (tt) REVERT: E 324 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7553 (tp) REVERT: E 328 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7786 (tt) REVERT: E 417 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3894 (tt) REVERT: F 98 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7507 (mtp) REVERT: F 230 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8109 (pt) REVERT: F 254 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8125 (tt) REVERT: F 338 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8297 (pttp) REVERT: F 349 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8424 (m) outliers start: 157 outliers final: 77 residues processed: 328 average time/residue: 1.2604 time to fit residues: 462.5477 Evaluate side-chains 274 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 173 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 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 315 ASP 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 374 GLU Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 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 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 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 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 328 LEU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 173 TYR 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 271 THR Chi-restraints excluded: chain D residue 302 ASP 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 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 324 LEU Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 404 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 129 ILE 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 443 ILE Chi-restraints excluded: chain F residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 200 optimal weight: 0.0670 overall best weight: 1.7122 ------------------------------------------------------------------------------- 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 D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.185311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151063 restraints weight = 19066.794| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.62 r_work: 0.3527 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16983 Z= 0.135 Angle : 0.592 11.600 23087 Z= 0.305 Chirality : 0.046 0.269 2612 Planarity : 0.004 0.049 2974 Dihedral : 11.131 88.878 2563 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.95 % Favored : 93.91 % Rotamer: Outliers : 8.60 % Allowed : 32.77 % Favored : 58.63 % 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: -1.89 (0.18), residues: 2117 helix: -1.85 (0.32), residues: 228 sheet: -1.23 (0.22), residues: 466 loop : -1.17 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 406 HIS 0.012 0.001 HIS A 233 PHE 0.019 0.001 PHE F 111 TYR 0.013 0.001 TYR F 241 ARG 0.007 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 194) hydrogen bonds : angle 5.89485 ( 501) covalent geometry : bond 0.00319 (16983) covalent geometry : angle 0.59188 (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 330 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 176 time to evaluate : 1.879 Fit side-chains REVERT: A 98 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7677 (mtp) REVERT: A 142 LYS cc_start: 0.8169 (pttp) cc_final: 0.7626 (pptt) REVERT: A 219 LYS cc_start: 0.7032 (ttpp) cc_final: 0.6736 (ttmt) REVERT: A 234 HIS cc_start: 0.7500 (m90) cc_final: 0.7085 (m90) REVERT: A 240 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.5978 (p0) REVERT: A 254 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8010 (tt) REVERT: A 265 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6059 (ttt-90) REVERT: A 328 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7724 (tt) REVERT: A 367 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.8041 (m) REVERT: B 109 ARG cc_start: 0.8240 (ptt180) cc_final: 0.7710 (ptm160) REVERT: B 142 LYS cc_start: 0.7455 (tmmt) cc_final: 0.6803 (tmmt) REVERT: B 204 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: B 219 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.7018 (ptpt) REVERT: B 241 TYR cc_start: 0.4788 (OUTLIER) cc_final: 0.3923 (t80) REVERT: B 244 GLN cc_start: 0.7416 (mp10) cc_final: 0.6722 (mm110) REVERT: B 254 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8162 (tt) REVERT: B 414 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7837 (mtt180) REVERT: C 112 SER cc_start: 0.8817 (p) cc_final: 0.8550 (m) REVERT: C 254 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8217 (tt) REVERT: C 303 ILE cc_start: 0.6135 (OUTLIER) cc_final: 0.5861 (tt) REVERT: C 335 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8753 (tt0) REVERT: C 338 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8096 (pttp) REVERT: C 438 ARG cc_start: 0.6333 (mpt180) cc_final: 0.6067 (mpt180) REVERT: D 98 MET cc_start: 0.7944 (mtp) cc_final: 0.7652 (mtm) REVERT: D 142 LYS cc_start: 0.7479 (ptmm) cc_final: 0.7157 (pptt) REVERT: D 234 HIS cc_start: 0.7370 (m90) cc_final: 0.6922 (m90) REVERT: D 270 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7685 (mm) REVERT: D 382 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7782 (tm-30) REVERT: E 138 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7818 (ttt-90) REVERT: E 142 LYS cc_start: 0.7598 (tttp) cc_final: 0.6962 (tmmt) REVERT: E 172 TYR cc_start: 0.6389 (t80) cc_final: 0.5940 (t80) REVERT: E 234 HIS cc_start: 0.7301 (m90) cc_final: 0.6784 (m90) REVERT: E 245 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8086 (mtmm) REVERT: E 254 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8053 (tt) REVERT: E 328 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7791 (tt) REVERT: F 98 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7541 (mtp) REVERT: F 254 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8117 (tt) REVERT: F 338 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8475 (pttp) REVERT: F 420 ASP cc_start: 0.6472 (p0) cc_final: 0.6033 (p0) outliers start: 154 outliers final: 97 residues processed: 308 average time/residue: 1.1325 time to fit residues: 392.0795 Evaluate side-chains 287 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 167 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 244 GLN 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 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 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 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 134 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 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 335 GLN Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 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 222 THR 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 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 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 404 ILE Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 245 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 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 235 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 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 443 ILE 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: 0.9980 chunk 36 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 185 optimal weight: 0.0870 chunk 118 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 202 optimal weight: 0.0070 chunk 67 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.185551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151339 restraints weight = 18964.769| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.62 r_work: 0.3534 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16983 Z= 0.130 Angle : 0.585 10.917 23087 Z= 0.301 Chirality : 0.046 0.269 2612 Planarity : 0.004 0.049 2974 Dihedral : 10.897 85.908 2559 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 8.82 % Allowed : 32.94 % Favored : 58.24 % 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: -1.81 (0.18), residues: 2117 helix: -1.76 (0.33), residues: 227 sheet: -1.20 (0.22), residues: 477 loop : -1.10 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 406 HIS 0.012 0.001 HIS A 233 PHE 0.019 0.001 PHE F 111 TYR 0.013 0.001 TYR E 357 ARG 0.007 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 194) hydrogen bonds : angle 5.81754 ( 501) covalent geometry : bond 0.00307 (16983) covalent geometry : angle 0.58541 (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 334 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 176 time to evaluate : 1.724 Fit side-chains REVERT: A 98 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7687 (mtp) REVERT: A 142 LYS cc_start: 0.8147 (pttp) cc_final: 0.7615 (pptt) REVERT: A 219 LYS cc_start: 0.7054 (ttpp) cc_final: 0.6833 (ttmt) REVERT: A 234 HIS cc_start: 0.7499 (m90) cc_final: 0.7083 (m90) REVERT: A 240 ASP cc_start: 0.6321 (OUTLIER) cc_final: 0.5980 (p0) REVERT: A 254 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 265 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6037 (ttt-90) REVERT: A 328 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7722 (tt) REVERT: A 367 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7994 (m) REVERT: B 109 ARG cc_start: 0.8248 (ptt180) cc_final: 0.7739 (ptm160) REVERT: B 142 LYS cc_start: 0.7515 (tmmt) cc_final: 0.6859 (tmmt) REVERT: B 219 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6980 (ptpt) REVERT: B 241 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.3877 (t80) REVERT: B 244 GLN cc_start: 0.7432 (mp10) cc_final: 0.6742 (mm110) REVERT: B 254 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8162 (tt) REVERT: B 414 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7798 (mtt180) REVERT: C 112 SER cc_start: 0.8802 (p) cc_final: 0.8554 (m) REVERT: C 254 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8169 (tt) REVERT: C 303 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5894 (tt) REVERT: C 335 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: C 338 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8117 (pttp) REVERT: C 438 ARG cc_start: 0.6377 (mpt180) cc_final: 0.6102 (mpt180) REVERT: D 98 MET cc_start: 0.7953 (mtp) cc_final: 0.7629 (mtm) REVERT: D 142 LYS cc_start: 0.7440 (ptmm) cc_final: 0.7169 (pptt) REVERT: D 184 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7230 (mmm) REVERT: D 234 HIS cc_start: 0.7385 (m90) cc_final: 0.6962 (m90) REVERT: D 254 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8154 (tt) REVERT: D 270 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7728 (mm) REVERT: D 382 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7837 (tm-30) REVERT: D 414 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7331 (tpt-90) REVERT: E 138 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7825 (ttt-90) REVERT: E 142 LYS cc_start: 0.7602 (tttp) cc_final: 0.6993 (tmmt) REVERT: E 172 TYR cc_start: 0.6471 (t80) cc_final: 0.6011 (t80) REVERT: E 234 HIS cc_start: 0.7275 (m90) cc_final: 0.6750 (m90) REVERT: E 245 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8076 (mtmm) REVERT: E 254 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8070 (tt) REVERT: E 328 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7791 (tt) REVERT: F 98 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: F 254 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8118 (tt) REVERT: F 338 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8479 (pttp) REVERT: F 420 ASP cc_start: 0.6470 (p0) cc_final: 0.6027 (p0) outliers start: 158 outliers final: 97 residues processed: 310 average time/residue: 1.3264 time to fit residues: 465.8475 Evaluate side-chains 288 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 166 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 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 315 ASP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 414 ARG Chi-restraints excluded: chain 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 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 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 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 271 THR Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 300 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 335 GLN Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 126 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 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 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 347 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL 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 D residue 428 SER Chi-restraints excluded: chain D residue 441 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 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 349 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 126 LEU Chi-restraints excluded: chain F residue 129 ILE Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 308 THR 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 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: 2.9990 chunk 68 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 147 optimal weight: 0.0370 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.186133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151914 restraints weight = 18958.912| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.62 r_work: 0.3543 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16983 Z= 0.121 Angle : 0.577 11.123 23087 Z= 0.297 Chirality : 0.046 0.304 2612 Planarity : 0.004 0.048 2974 Dihedral : 10.436 76.047 2554 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.86 % Favored : 94.00 % Rotamer: Outliers : 8.04 % Allowed : 33.61 % Favored : 58.35 % 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: -1.74 (0.18), residues: 2117 helix: -1.67 (0.33), residues: 227 sheet: -1.17 (0.22), residues: 484 loop : -1.06 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 406 HIS 0.012 0.001 HIS E 233 PHE 0.020 0.001 PHE F 111 TYR 0.011 0.001 TYR E 357 ARG 0.006 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 194) hydrogen bonds : angle 5.74480 ( 501) covalent geometry : bond 0.00284 (16983) covalent geometry : angle 0.57696 (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 319 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 175 time to evaluate : 2.138 Fit side-chains REVERT: A 98 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7722 (mtp) REVERT: A 142 LYS cc_start: 0.8139 (pttp) cc_final: 0.7609 (pptt) REVERT: A 219 LYS cc_start: 0.6981 (ttpp) cc_final: 0.6767 (ttmt) REVERT: A 234 HIS cc_start: 0.7447 (m90) cc_final: 0.7047 (m90) REVERT: A 240 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.6080 (p0) REVERT: A 241 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.4302 (t80) REVERT: A 254 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8081 (tt) REVERT: A 265 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6017 (ttt-90) REVERT: A 328 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7725 (tt) REVERT: A 440 GLU cc_start: 0.6392 (tp30) cc_final: 0.6152 (tp30) REVERT: B 109 ARG cc_start: 0.8240 (ptt180) cc_final: 0.7738 (ptm160) REVERT: B 142 LYS cc_start: 0.7485 (tmmt) cc_final: 0.6824 (tmmt) REVERT: B 241 TYR cc_start: 0.4754 (OUTLIER) cc_final: 0.3858 (t80) REVERT: B 244 GLN cc_start: 0.7417 (mp10) cc_final: 0.6744 (mm110) REVERT: B 254 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8139 (tt) REVERT: B 414 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7762 (mtt180) REVERT: C 112 SER cc_start: 0.8798 (p) cc_final: 0.8559 (m) REVERT: C 142 LYS cc_start: 0.7748 (pptt) cc_final: 0.7200 (tttp) REVERT: C 254 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8160 (tt) REVERT: C 303 ILE cc_start: 0.6116 (OUTLIER) cc_final: 0.5827 (tt) REVERT: C 338 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8109 (pttm) REVERT: C 438 ARG cc_start: 0.6362 (mpt180) cc_final: 0.6077 (mpt180) REVERT: D 142 LYS cc_start: 0.7481 (ptmm) cc_final: 0.7174 (pptt) REVERT: D 184 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7192 (mmm) REVERT: D 234 HIS cc_start: 0.7478 (m90) cc_final: 0.7044 (m90) REVERT: D 246 MET cc_start: 0.8497 (mmp) cc_final: 0.8292 (mmt) REVERT: D 254 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8147 (tt) REVERT: D 270 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7743 (mm) REVERT: D 382 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7856 (tm-30) REVERT: D 414 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7323 (tpt-90) REVERT: E 92 ASN cc_start: 0.7298 (p0) cc_final: 0.6988 (t0) REVERT: E 138 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7811 (ttt-90) REVERT: E 142 LYS cc_start: 0.7619 (tttp) cc_final: 0.6992 (tmmt) REVERT: E 172 TYR cc_start: 0.6439 (t80) cc_final: 0.6045 (t80) REVERT: E 234 HIS cc_start: 0.7347 (m90) cc_final: 0.6708 (m90) REVERT: E 245 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7949 (mtmm) REVERT: E 254 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8078 (tt) REVERT: E 328 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7732 (tt) REVERT: F 98 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7493 (mtp) REVERT: F 254 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8095 (tt) REVERT: F 338 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8459 (pttp) REVERT: F 420 ASP cc_start: 0.6453 (p0) cc_final: 0.6021 (p0) outliers start: 144 outliers final: 96 residues processed: 298 average time/residue: 1.3763 time to fit residues: 461.8503 Evaluate side-chains 288 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 169 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 240 ASP 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 328 LEU Chi-restraints excluded: chain A residue 335 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 367 THR Chi-restraints excluded: chain A residue 414 ARG 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 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 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 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 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 417 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 126 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 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 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 356 GLU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 371 VAL 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 D residue 428 SER Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 241 TYR Chi-restraints excluded: chain E residue 244 GLN Chi-restraints excluded: chain E residue 245 LYS 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 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 235 VAL 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 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 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: 3.9990 chunk 203 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 233 HIS C 335 GLN D 233 HIS ** D 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.151989 restraints weight = 19069.782| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.62 r_work: 0.3542 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16983 Z= 0.124 Angle : 0.579 11.398 23087 Z= 0.297 Chirality : 0.046 0.292 2612 Planarity : 0.004 0.049 2974 Dihedral : 10.189 75.797 2552 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.81 % Favored : 94.05 % Rotamer: Outliers : 7.31 % Allowed : 34.51 % Favored : 58.18 % 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: -1.65 (0.18), residues: 2117 helix: -1.61 (0.33), residues: 227 sheet: -1.01 (0.23), residues: 463 loop : -1.04 (0.17), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 406 HIS 0.013 0.001 HIS E 233 PHE 0.021 0.001 PHE F 111 TYR 0.011 0.001 TYR E 357 ARG 0.005 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 194) hydrogen bonds : angle 5.71700 ( 501) covalent geometry : bond 0.00293 (16983) covalent geometry : angle 0.57924 (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 308 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 177 time to evaluate : 1.831 Fit side-chains REVERT: A 98 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7759 (mtp) REVERT: A 142 LYS cc_start: 0.8083 (pttp) cc_final: 0.7575 (pptt) REVERT: A 172 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.4261 (m-80) REVERT: A 219 LYS cc_start: 0.6945 (ttpp) cc_final: 0.6723 (ttmm) REVERT: A 234 HIS cc_start: 0.7464 (m90) cc_final: 0.7054 (m90) REVERT: A 241 TYR cc_start: 0.5575 (OUTLIER) cc_final: 0.4227 (t80) REVERT: A 254 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 265 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6029 (ttt-90) REVERT: A 328 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7666 (tt) REVERT: B 89 GLN cc_start: 0.7426 (tp40) cc_final: 0.5753 (tm-30) REVERT: B 109 ARG cc_start: 0.8303 (ptt180) cc_final: 0.7806 (ptm160) REVERT: B 142 LYS cc_start: 0.7591 (tmmt) cc_final: 0.6991 (tmmt) REVERT: B 241 TYR cc_start: 0.4763 (OUTLIER) cc_final: 0.3871 (t80) REVERT: B 244 GLN cc_start: 0.7440 (mp10) cc_final: 0.6757 (mm110) REVERT: B 254 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8103 (tt) REVERT: B 414 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7753 (mtt180) REVERT: B 440 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.4820 (pp20) REVERT: C 112 SER cc_start: 0.8798 (p) cc_final: 0.8569 (m) REVERT: C 142 LYS cc_start: 0.7635 (pptt) cc_final: 0.7349 (tttp) REVERT: C 254 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8138 (tt) REVERT: C 303 ILE cc_start: 0.6136 (OUTLIER) cc_final: 0.5897 (tt) REVERT: C 328 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7844 (tt) REVERT: C 338 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8096 (pttp) REVERT: C 417 LEU cc_start: 0.4080 (OUTLIER) cc_final: 0.3875 (mt) REVERT: C 438 ARG cc_start: 0.6292 (mpt180) cc_final: 0.6038 (mpt180) REVERT: D 142 LYS cc_start: 0.7466 (ptmm) cc_final: 0.7262 (pptt) REVERT: D 184 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7205 (mmm) REVERT: D 234 HIS cc_start: 0.7571 (m90) cc_final: 0.7107 (m90) REVERT: D 254 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8101 (tt) REVERT: D 270 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7771 (mm) REVERT: D 382 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7826 (tm-30) REVERT: D 414 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7434 (tpt-90) REVERT: E 92 ASN cc_start: 0.7197 (p0) cc_final: 0.6904 (t0) REVERT: E 138 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7813 (ttt-90) REVERT: E 142 LYS cc_start: 0.7633 (tttp) cc_final: 0.7017 (tmmt) REVERT: E 232 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7436 (m110) REVERT: E 234 HIS cc_start: 0.7308 (m90) cc_final: 0.6654 (m90) REVERT: E 245 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7938 (mtmm) REVERT: E 254 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8052 (tt) REVERT: E 328 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7739 (tt) REVERT: E 442 ASP cc_start: 0.7855 (m-30) cc_final: 0.7648 (m-30) REVERT: F 98 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7526 (mtp) REVERT: F 234 HIS cc_start: 0.7332 (m-70) cc_final: 0.7108 (m-70) REVERT: F 254 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8034 (tt) REVERT: F 338 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8490 (pttp) REVERT: F 420 ASP cc_start: 0.6444 (p0) cc_final: 0.6018 (p0) outliers start: 131 outliers final: 86 residues processed: 289 average time/residue: 1.1378 time to fit residues: 370.3132 Evaluate side-chains 281 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 168 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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 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 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 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 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 341 ARG Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 414 ARG Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 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 346 THR Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 129 ILE 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 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 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 346 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 356 GLU 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 404 ILE Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 ASN 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 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 404 ILE 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 235 VAL 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 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 185 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 162 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 chunk 152 optimal weight: 7.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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 411 ASN ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.183183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148832 restraints weight = 18970.118| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.59 r_work: 0.3500 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16983 Z= 0.180 Angle : 0.652 11.324 23087 Z= 0.333 Chirality : 0.048 0.347 2612 Planarity : 0.004 0.048 2974 Dihedral : 10.757 76.661 2542 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 7.09 % Allowed : 34.90 % Favored : 58.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (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: -1.81 (0.18), residues: 2117 helix: -1.76 (0.32), residues: 228 sheet: -1.22 (0.22), residues: 484 loop : -1.10 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 406 HIS 0.014 0.002 HIS D 233 PHE 0.021 0.002 PHE F 111 TYR 0.017 0.001 TYR F 241 ARG 0.004 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 194) hydrogen bonds : angle 5.99145 ( 501) covalent geometry : bond 0.00431 (16983) covalent geometry : angle 0.65183 (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 298 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 171 time to evaluate : 1.726 Fit side-chains REVERT: A 98 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7781 (mtp) REVERT: A 142 LYS cc_start: 0.8143 (pttp) cc_final: 0.7628 (pptt) REVERT: A 172 TYR cc_start: 0.4638 (OUTLIER) cc_final: 0.4263 (m-80) REVERT: A 219 LYS cc_start: 0.7130 (ttpp) cc_final: 0.6797 (ttmm) REVERT: A 234 HIS cc_start: 0.7564 (m90) cc_final: 0.7187 (m90) REVERT: A 241 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.4281 (t80) REVERT: A 265 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6133 (ttt-90) REVERT: A 328 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7762 (tt) REVERT: A 361 LYS cc_start: 0.7020 (mttt) cc_final: 0.6742 (mttm) REVERT: A 367 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8072 (m) REVERT: A 414 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6220 (ptm-80) REVERT: A 440 GLU cc_start: 0.6455 (tp30) cc_final: 0.6195 (tp30) REVERT: B 109 ARG cc_start: 0.8362 (ptt180) cc_final: 0.7833 (ptm160) REVERT: B 142 LYS cc_start: 0.7581 (tmmt) cc_final: 0.6981 (tmmt) REVERT: B 241 TYR cc_start: 0.4800 (OUTLIER) cc_final: 0.3897 (t80) REVERT: B 244 GLN cc_start: 0.7666 (mp10) cc_final: 0.6917 (mm110) REVERT: B 440 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5019 (pp20) REVERT: C 112 SER cc_start: 0.8820 (p) cc_final: 0.8549 (m) REVERT: C 142 LYS cc_start: 0.7676 (pptt) cc_final: 0.7400 (tttp) REVERT: C 230 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.7843 (pt) REVERT: C 254 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8084 (tt) REVERT: C 303 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5748 (tt) REVERT: C 328 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7953 (tt) REVERT: C 338 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8217 (pttm) REVERT: D 142 LYS cc_start: 0.7524 (ptmm) cc_final: 0.7202 (pptt) REVERT: D 184 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7270 (mmm) REVERT: D 234 HIS cc_start: 0.7418 (m90) cc_final: 0.7005 (m90) REVERT: D 254 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8031 (tt) REVERT: D 270 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7794 (mm) REVERT: D 382 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7758 (tm-30) REVERT: D 414 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7443 (tpt-90) REVERT: E 92 ASN cc_start: 0.7168 (p0) cc_final: 0.6909 (t0) REVERT: E 138 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7870 (ttt-90) REVERT: E 142 LYS cc_start: 0.7664 (tttp) cc_final: 0.7007 (tmmt) REVERT: E 232 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7122 (m-40) REVERT: E 234 HIS cc_start: 0.7389 (m90) cc_final: 0.6726 (m90) REVERT: E 245 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.8104 (mtmm) REVERT: E 328 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7843 (tt) REVERT: E 442 ASP cc_start: 0.7927 (m-30) cc_final: 0.7699 (m-30) REVERT: F 98 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7544 (mtp) REVERT: F 338 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8566 (pttp) REVERT: F 420 ASP cc_start: 0.6621 (p0) cc_final: 0.6125 (p0) outliers start: 127 outliers final: 86 residues processed: 278 average time/residue: 1.1817 time to fit residues: 369.3233 Evaluate side-chains 276 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 166 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 328 LEU Chi-restraints excluded: chain A residue 335 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 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 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 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 420 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 258 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 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 126 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 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 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 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 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 138 ARG Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 ASN 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 274 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 404 ILE 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 235 VAL Chi-restraints excluded: chain F residue 237 VAL 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 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: 1.9990 chunk 204 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 233 HIS C 421 HIS D 233 HIS ** E 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.184489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150322 restraints weight = 18955.141| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.60 r_work: 0.3523 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16983 Z= 0.141 Angle : 0.612 10.918 23087 Z= 0.313 Chirality : 0.046 0.328 2612 Planarity : 0.004 0.050 2974 Dihedral : 10.395 75.800 2540 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.05 % Favored : 93.81 % Rotamer: Outliers : 6.92 % Allowed : 35.01 % Favored : 58.07 % 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: -1.73 (0.18), residues: 2117 helix: -1.64 (0.32), residues: 228 sheet: -1.19 (0.22), residues: 475 loop : -1.05 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 406 HIS 0.013 0.002 HIS A 233 PHE 0.025 0.001 PHE B 269 TYR 0.013 0.001 TYR E 357 ARG 0.005 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 194) hydrogen bonds : angle 5.88648 ( 501) covalent geometry : bond 0.00334 (16983) covalent geometry : angle 0.61199 (23087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10616.65 seconds wall clock time: 186 minutes 46.12 seconds (11206.12 seconds total)