Starting phenix.real_space_refine on Thu Mar 5 00:55:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lt0_0966/03_2026/6lt0_0966.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lt0_0966/03_2026/6lt0_0966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lt0_0966/03_2026/6lt0_0966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lt0_0966/03_2026/6lt0_0966.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lt0_0966/03_2026/6lt0_0966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lt0_0966/03_2026/6lt0_0966.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 11438 2.51 5 N 3052 2.21 5 O 3196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17774 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2693 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 337} Chain breaks: 6 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3134 Classifications: {'peptide': 386} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 370} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3060 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 5 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2693 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 337} Chain breaks: 6 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3134 Classifications: {'peptide': 386} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 370} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3060 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 5 Time building chain proxies: 3.78, per 1000 atoms: 0.21 Number of scatterers: 17774 At special positions: 0 Unit cell: (157.028, 155.967, 89.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3196 8.00 N 3052 7.00 C 11438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 790.1 milliseconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 28 sheets defined 36.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 440 through 453 removed outlier: 4.708A pdb=" N PHE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.991A pdb=" N GLN B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 removed outlier: 4.236A pdb=" N ILE B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.820A pdb=" N ALA B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 188 removed outlier: 4.180A pdb=" N LEU B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.573A pdb=" N SER B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.850A pdb=" N PHE B 370 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 371 " --> pdb=" O THR B 368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 372 " --> pdb=" O ASN B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 372' Processing helix chain 'B' and resid 702 through 715 Processing helix chain 'B' and resid 720 through 730 Processing helix chain 'B' and resid 739 through 751 removed outlier: 3.765A pdb=" N VAL B 743 " --> pdb=" O ASP B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.515A pdb=" N LYS B 779 " --> pdb=" O MET B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 801 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 825 through 831 Processing helix chain 'B' and resid 840 through 864 removed outlier: 3.589A pdb=" N GLN B 853 " --> pdb=" O SER B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 869 removed outlier: 3.802A pdb=" N HIS B 868 " --> pdb=" O CYS B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 891 Processing helix chain 'B' and resid 897 through 916 removed outlier: 4.042A pdb=" N GLU B 907 " --> pdb=" O GLN B 903 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 68 removed outlier: 3.803A pdb=" N ASN C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 127 through 148 removed outlier: 4.157A pdb=" N ASP C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 193 removed outlier: 4.531A pdb=" N GLY C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU C 179 " --> pdb=" O MET C 175 " (cutoff:3.500A) Proline residue: C 182 - end of helix removed outlier: 3.805A pdb=" N GLU C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.631A pdb=" N ASP C 203 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 204 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 200 through 204' Processing helix chain 'C' and resid 215 through 230 removed outlier: 3.652A pdb=" N ILE C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.566A pdb=" N LYS C 261 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 300 removed outlier: 3.804A pdb=" N MET C 299 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 Processing helix chain 'C' and resid 375 through 385 removed outlier: 4.491A pdb=" N PHE C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 420 removed outlier: 3.568A pdb=" N THR C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.653A pdb=" N LEU C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 455 removed outlier: 4.544A pdb=" N ILE C 447 " --> pdb=" O GLY C 443 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 464 removed outlier: 3.681A pdb=" N PHE C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 453 removed outlier: 4.709A pdb=" N PHE D 446 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.991A pdb=" N GLN E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 167 removed outlier: 4.236A pdb=" N ILE E 165 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 174 removed outlier: 3.820A pdb=" N ALA E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 188 removed outlier: 4.180A pdb=" N LEU E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 345 removed outlier: 4.573A pdb=" N SER E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.850A pdb=" N PHE E 370 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 371 " --> pdb=" O THR E 368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 372 " --> pdb=" O ASN E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 372' Processing helix chain 'E' and resid 702 through 715 Processing helix chain 'E' and resid 720 through 730 Processing helix chain 'E' and resid 739 through 751 removed outlier: 3.764A pdb=" N VAL E 743 " --> pdb=" O ASP E 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 754 No H-bonds generated for 'chain 'E' and resid 752 through 754' Processing helix chain 'E' and resid 775 through 780 removed outlier: 3.514A pdb=" N LYS E 779 " --> pdb=" O MET E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 801 Processing helix chain 'E' and resid 802 through 804 No H-bonds generated for 'chain 'E' and resid 802 through 804' Processing helix chain 'E' and resid 825 through 831 Processing helix chain 'E' and resid 840 through 864 removed outlier: 3.589A pdb=" N GLN E 853 " --> pdb=" O SER E 849 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 869 removed outlier: 3.802A pdb=" N HIS E 868 " --> pdb=" O CYS E 864 " (cutoff:3.500A) Processing helix chain 'E' and resid 876 through 891 Processing helix chain 'E' and resid 897 through 916 removed outlier: 4.042A pdb=" N GLU E 907 " --> pdb=" O GLN E 903 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 915 " --> pdb=" O LEU E 911 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 68 removed outlier: 3.803A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 127 through 148 removed outlier: 4.157A pdb=" N ASP F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 193 removed outlier: 4.532A pdb=" N GLY F 178 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU F 179 " --> pdb=" O MET F 175 " (cutoff:3.500A) Proline residue: F 182 - end of helix removed outlier: 3.806A pdb=" N GLU F 185 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 187 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.631A pdb=" N ASP F 203 " --> pdb=" O ASP F 200 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR F 204 " --> pdb=" O ILE F 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 200 through 204' Processing helix chain 'F' and resid 215 through 230 removed outlier: 3.652A pdb=" N ILE F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 252 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.566A pdb=" N LYS F 261 " --> pdb=" O PRO F 257 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYS F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 300 removed outlier: 3.804A pdb=" N MET F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR F 300 " --> pdb=" O ARG F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 337 Processing helix chain 'F' and resid 375 through 385 removed outlier: 4.492A pdb=" N PHE F 385 " --> pdb=" O LEU F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 420 removed outlier: 3.568A pdb=" N THR F 420 " --> pdb=" O ILE F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 437 removed outlier: 3.652A pdb=" N LEU F 433 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 455 removed outlier: 4.544A pdb=" N ILE F 447 " --> pdb=" O GLY F 443 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 464 removed outlier: 3.682A pdb=" N PHE F 462 " --> pdb=" O GLY F 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 40 removed outlier: 4.947A pdb=" N LEU A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 423 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 419 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET A 410 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 53 removed outlier: 5.510A pdb=" N LEU A 49 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 60 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN A 51 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA A 58 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 53 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 78 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN A 70 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS A 76 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 92 removed outlier: 4.068A pdb=" N ALA A 89 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 127 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 3.625A pdb=" N VAL A 147 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.976A pdb=" N LYS A 167 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.600A pdb=" N VAL A 187 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 230 removed outlier: 3.605A pdb=" N SER A 227 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 246 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU A 245 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 276 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 247 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 291 through 292 removed outlier: 4.217A pdb=" N VAL A 306 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 329 through 332 removed outlier: 4.027A pdb=" N GLN A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 347 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 348 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.867A pdb=" N SER B 61 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 156 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 153 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B 135 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 133 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER B 159 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY B 131 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN B 116 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 115 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 81 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 782 through 785 Processing sheet with id=AB3, first strand: chain 'B' and resid 817 through 819 removed outlier: 3.691A pdb=" N LEU B 817 " --> pdb=" O TYR B 935 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 819 " --> pdb=" O PHE B 933 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.263A pdb=" N THR C 15 " --> pdb=" O ALA C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 280 through 281 Processing sheet with id=AB6, first strand: chain 'D' and resid 35 through 40 removed outlier: 4.947A pdb=" N LEU D 427 " --> pdb=" O SER D 423 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 423 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 419 " --> pdb=" O TRP D 431 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET D 410 " --> pdb=" O CYS D 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 53 removed outlier: 5.510A pdb=" N LEU D 49 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA D 60 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN D 51 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA D 58 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 53 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 78 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN D 70 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS D 76 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 87 through 92 removed outlier: 4.069A pdb=" N ALA D 89 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN D 127 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 141 through 142 removed outlier: 3.625A pdb=" N VAL D 147 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 156 through 157 removed outlier: 3.975A pdb=" N LYS D 167 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.600A pdb=" N VAL D 187 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.605A pdb=" N SER D 227 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE D 246 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 245 " --> pdb=" O LYS D 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS D 276 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 247 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 291 through 292 removed outlier: 4.217A pdb=" N VAL D 306 " --> pdb=" O ILE D 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 329 through 332 removed outlier: 4.026A pdb=" N GLN D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG D 347 " --> pdb=" O SER D 339 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 348 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.867A pdb=" N SER E 61 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 156 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE E 153 " --> pdb=" O HIS E 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR E 135 " --> pdb=" O MET E 155 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE E 133 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER E 159 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY E 131 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN E 116 " --> pdb=" O ALA E 134 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU E 115 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP F 81 " --> pdb=" O ILE F 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 782 through 785 Processing sheet with id=AC8, first strand: chain 'E' and resid 817 through 819 removed outlier: 3.692A pdb=" N LEU E 817 " --> pdb=" O TYR E 935 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS E 819 " --> pdb=" O PHE E 933 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 14 through 17 removed outlier: 6.262A pdb=" N THR F 15 " --> pdb=" O ALA F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 280 through 281 650 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5474 1.34 - 1.46: 3097 1.46 - 1.57: 9439 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 18136 Sorted by residual: bond pdb=" C ILE F 181 " pdb=" N PRO F 182 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.22e+01 bond pdb=" C ILE C 181 " pdb=" N PRO C 182 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.20e-02 6.94e+03 2.22e+01 bond pdb=" C TYR E 112 " pdb=" N PRO E 113 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.53e+00 bond pdb=" C TYR B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.50e+00 bond pdb=" C PRO E 107 " pdb=" N PRO E 108 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.42e+00 ... (remaining 18131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 23767 2.73 - 5.45: 605 5.45 - 8.18: 114 8.18 - 10.90: 22 10.90 - 13.63: 10 Bond angle restraints: 24518 Sorted by residual: angle pdb=" C ILE C 172 " pdb=" N ILE C 173 " pdb=" CA ILE C 173 " ideal model delta sigma weight residual 120.33 124.57 -4.24 8.00e-01 1.56e+00 2.81e+01 angle pdb=" C ILE F 172 " pdb=" N ILE F 173 " pdb=" CA ILE F 173 " ideal model delta sigma weight residual 120.33 124.55 -4.22 8.00e-01 1.56e+00 2.78e+01 angle pdb=" C LEU D 145 " pdb=" N ASP D 146 " pdb=" CA ASP D 146 " ideal model delta sigma weight residual 122.46 129.24 -6.78 1.41e+00 5.03e-01 2.31e+01 angle pdb=" C LEU A 145 " pdb=" N ASP A 146 " pdb=" CA ASP A 146 " ideal model delta sigma weight residual 122.46 129.21 -6.75 1.41e+00 5.03e-01 2.29e+01 angle pdb=" C GLY C 21 " pdb=" N LYS C 22 " pdb=" CA LYS C 22 " ideal model delta sigma weight residual 120.82 127.23 -6.41 1.47e+00 4.63e-01 1.90e+01 ... (remaining 24513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 9958 15.40 - 30.80: 610 30.80 - 46.21: 208 46.21 - 61.61: 10 61.61 - 77.01: 18 Dihedral angle restraints: 10804 sinusoidal: 4322 harmonic: 6482 Sorted by residual: dihedral pdb=" CA LEU A 218 " pdb=" C LEU A 218 " pdb=" N LEU A 219 " pdb=" CA LEU A 219 " ideal model delta harmonic sigma weight residual -180.00 -133.33 -46.67 0 5.00e+00 4.00e-02 8.71e+01 dihedral pdb=" CA LEU D 218 " pdb=" C LEU D 218 " pdb=" N LEU D 219 " pdb=" CA LEU D 219 " ideal model delta harmonic sigma weight residual -180.00 -133.39 -46.61 0 5.00e+00 4.00e-02 8.69e+01 dihedral pdb=" CA ASP D 292 " pdb=" C ASP D 292 " pdb=" N GLU D 293 " pdb=" CA GLU D 293 " ideal model delta harmonic sigma weight residual -180.00 -144.21 -35.79 0 5.00e+00 4.00e-02 5.12e+01 ... (remaining 10801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1927 0.052 - 0.103: 659 0.103 - 0.155: 215 0.155 - 0.207: 29 0.207 - 0.258: 8 Chirality restraints: 2838 Sorted by residual: chirality pdb=" CB VAL C 195 " pdb=" CA VAL C 195 " pdb=" CG1 VAL C 195 " pdb=" CG2 VAL C 195 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB VAL F 195 " pdb=" CA VAL F 195 " pdb=" CG1 VAL F 195 " pdb=" CG2 VAL F 195 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL E 104 " pdb=" CA VAL E 104 " pdb=" CG1 VAL E 104 " pdb=" CG2 VAL E 104 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2835 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 107 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO E 108 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 107 " -0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 108 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 218 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C LEU D 218 " -0.055 2.00e-02 2.50e+03 pdb=" O LEU D 218 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU D 219 " 0.019 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 61 2.50 - 3.10: 11297 3.10 - 3.70: 26318 3.70 - 4.30: 36526 4.30 - 4.90: 61858 Nonbonded interactions: 136060 Sorted by model distance: nonbonded pdb=" O ARG B 834 " pdb=" NH2 ARG F 431 " model vdw 1.898 3.120 nonbonded pdb=" CG ASN B 896 " pdb=" OE1 GLN F 368 " model vdw 1.912 3.270 nonbonded pdb=" NH2 ARG C 431 " pdb=" OD2 ASP E 832 " model vdw 1.957 3.120 nonbonded pdb=" ND2 ASN B 896 " pdb=" OE1 GLN F 368 " model vdw 2.007 3.120 nonbonded pdb=" O GLU E 181 " pdb=" OG1 THR E 185 " model vdw 2.276 3.040 ... (remaining 136055 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.290 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 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 : 0.005 0.060 18136 Z= 0.248 Angle : 1.085 13.626 24518 Z= 0.567 Chirality : 0.058 0.258 2838 Planarity : 0.007 0.081 3058 Dihedral : 11.856 77.009 6580 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.34 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.35 (0.14), residues: 2144 helix: -3.40 (0.12), residues: 708 sheet: -2.99 (0.21), residues: 498 loop : -3.91 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 56 TYR 0.025 0.002 TYR B 757 PHE 0.022 0.003 PHE F 99 TRP 0.029 0.003 TRP A 118 HIS 0.013 0.002 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00550 (18136) covalent geometry : angle 1.08496 (24518) hydrogen bonds : bond 0.19828 ( 650) hydrogen bonds : angle 10.24809 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8387 (mp) cc_final: 0.8186 (pp) REVERT: A 118 TRP cc_start: 0.7579 (m-10) cc_final: 0.6995 (m-10) REVERT: A 200 LEU cc_start: 0.7215 (tt) cc_final: 0.6888 (mt) REVERT: B 363 LYS cc_start: 0.6737 (mmtp) cc_final: 0.6341 (tttp) REVERT: B 767 TRP cc_start: 0.6338 (t60) cc_final: 0.5915 (t60) REVERT: C 64 ASN cc_start: 0.7286 (m110) cc_final: 0.7054 (m-40) REVERT: C 184 MET cc_start: 0.8523 (tmt) cc_final: 0.8226 (tmm) REVERT: C 191 LYS cc_start: 0.7387 (ttpt) cc_final: 0.6944 (tmtt) REVERT: C 414 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7590 (mmmt) REVERT: D 94 PRO cc_start: 0.2150 (Cg_exo) cc_final: 0.1754 (Cg_endo) REVERT: E 155 MET cc_start: 0.4543 (ptt) cc_final: 0.4021 (mtm) REVERT: E 162 GLN cc_start: 0.5024 (tp-100) cc_final: 0.4587 (pm20) REVERT: E 888 LEU cc_start: 0.4505 (mp) cc_final: 0.4265 (mp) REVERT: F 49 THR cc_start: 0.3656 (p) cc_final: 0.3332 (t) REVERT: F 94 ILE cc_start: 0.7359 (mt) cc_final: 0.6143 (mt) REVERT: F 184 MET cc_start: 0.5608 (tmt) cc_final: 0.5307 (tmm) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.1596 time to fit residues: 112.9397 Evaluate side-chains 249 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.0000 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS A 426 HIS B 106 HIS ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN B 922 HIS C 65 HIS C 137 HIS C 281 GLN C 460 HIS D 143 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 426 HIS D 433 ASN E 106 HIS E 163 HIS E 168 GLN E 340 HIS E 366 HIS ** E 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 798 HIS E 846 HIS E 872 HIS E 922 HIS ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN F 460 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.227362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157298 restraints weight = 29996.401| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.02 r_work: 0.3840 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18136 Z= 0.146 Angle : 0.742 10.076 24518 Z= 0.376 Chirality : 0.046 0.177 2838 Planarity : 0.006 0.062 3058 Dihedral : 6.340 47.186 2372 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.77 % Favored : 89.13 % Rotamer: Outliers : 2.91 % Allowed : 11.57 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.15), residues: 2144 helix: -1.51 (0.16), residues: 744 sheet: -2.36 (0.23), residues: 440 loop : -3.82 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 441 TYR 0.019 0.001 TYR D 55 PHE 0.028 0.002 PHE C 61 TRP 0.022 0.002 TRP A 148 HIS 0.013 0.001 HIS E 366 Details of bonding type rmsd covalent geometry : bond 0.00325 (18136) covalent geometry : angle 0.74200 (24518) hydrogen bonds : bond 0.04321 ( 650) hydrogen bonds : angle 6.35437 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 291 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 TRP cc_start: 0.7571 (m-10) cc_final: 0.6840 (m-90) REVERT: A 200 LEU cc_start: 0.7441 (tt) cc_final: 0.7217 (mt) REVERT: A 271 THR cc_start: 0.6867 (m) cc_final: 0.6621 (m) REVERT: B 363 LYS cc_start: 0.7468 (mmtp) cc_final: 0.7166 (tttp) REVERT: B 767 TRP cc_start: 0.6770 (t60) cc_final: 0.6268 (t60) REVERT: C 64 ASN cc_start: 0.7393 (m110) cc_final: 0.6848 (m-40) REVERT: C 98 ILE cc_start: 0.7175 (mm) cc_final: 0.6705 (pt) REVERT: C 184 MET cc_start: 0.8752 (tmt) cc_final: 0.8325 (tmm) REVERT: C 191 LYS cc_start: 0.7478 (ttpt) cc_final: 0.7048 (tmtt) REVERT: C 298 VAL cc_start: 0.9163 (t) cc_final: 0.8817 (m) REVERT: C 334 SER cc_start: 0.7748 (OUTLIER) cc_final: 0.7194 (m) REVERT: C 414 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7769 (mmmt) REVERT: D 216 LYS cc_start: 0.1579 (ttpt) cc_final: 0.1207 (mttt) REVERT: D 305 TYR cc_start: 0.6341 (m-80) cc_final: 0.6097 (m-80) REVERT: E 116 ASN cc_start: 0.5979 (p0) cc_final: 0.5501 (m-40) REVERT: E 155 MET cc_start: 0.4710 (ptt) cc_final: 0.4145 (mtm) REVERT: E 372 PHE cc_start: 0.5811 (p90) cc_final: 0.4956 (p90) REVERT: E 853 GLN cc_start: 0.8533 (tt0) cc_final: 0.8250 (tt0) REVERT: E 861 TYR cc_start: 0.6499 (t80) cc_final: 0.5962 (t80) REVERT: F 49 THR cc_start: 0.3074 (p) cc_final: 0.2602 (t) REVERT: F 85 PHE cc_start: 0.5896 (t80) cc_final: 0.5221 (t80) REVERT: F 184 MET cc_start: 0.5193 (tmt) cc_final: 0.4965 (tmm) REVERT: F 191 LYS cc_start: 0.4832 (ttpt) cc_final: 0.4595 (tppt) REVERT: F 249 ARG cc_start: 0.5534 (mtt90) cc_final: 0.5195 (ptt180) REVERT: F 260 ARG cc_start: 0.4220 (mtt90) cc_final: 0.2656 (ttp80) REVERT: F 317 GLN cc_start: 0.7207 (tt0) cc_final: 0.6427 (tm-30) REVERT: F 318 MET cc_start: 0.6375 (mmm) cc_final: 0.5944 (ttm) REVERT: F 407 ARG cc_start: 0.8400 (mtt180) cc_final: 0.7881 (ptp-110) outliers start: 57 outliers final: 33 residues processed: 334 average time/residue: 0.1320 time to fit residues: 66.7416 Evaluate side-chains 261 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain E residue 713 PHE Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 798 HIS Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 215 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 84 optimal weight: 0.3980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 162 GLN B 369 ASN C 65 HIS D 83 HIS ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS F 64 ASN F 383 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.220727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.145586 restraints weight = 30151.068| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.48 r_work: 0.3724 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 18136 Z= 0.264 Angle : 0.838 11.801 24518 Z= 0.423 Chirality : 0.051 0.265 2838 Planarity : 0.006 0.064 3058 Dihedral : 6.321 47.478 2372 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.13 % Favored : 87.78 % Rotamer: Outliers : 4.79 % Allowed : 13.51 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.16), residues: 2144 helix: -0.93 (0.18), residues: 744 sheet: -2.36 (0.22), residues: 454 loop : -3.61 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 805 TYR 0.026 0.002 TYR B 935 PHE 0.026 0.003 PHE C 427 TRP 0.037 0.002 TRP A 148 HIS 0.018 0.002 HIS E 798 Details of bonding type rmsd covalent geometry : bond 0.00621 (18136) covalent geometry : angle 0.83756 (24518) hydrogen bonds : bond 0.04780 ( 650) hydrogen bonds : angle 5.99948 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 253 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8200 (pt) REVERT: A 78 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7756 (pp) REVERT: A 216 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7514 (tptp) REVERT: A 271 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7107 (m) REVERT: A 311 MET cc_start: 0.8189 (ttm) cc_final: 0.7985 (ttt) REVERT: B 95 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.4156 (tmm) REVERT: B 363 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7453 (tttp) REVERT: C 64 ASN cc_start: 0.7617 (m110) cc_final: 0.7027 (m-40) REVERT: C 184 MET cc_start: 0.8752 (tmt) cc_final: 0.8360 (tmm) REVERT: C 191 LYS cc_start: 0.7807 (ttpt) cc_final: 0.7433 (tttm) REVERT: C 321 CYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6383 (t) REVERT: C 333 ARG cc_start: 0.7055 (ttm170) cc_final: 0.6672 (mmt-90) REVERT: C 334 SER cc_start: 0.7625 (OUTLIER) cc_final: 0.7338 (m) REVERT: C 414 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8089 (mmtt) REVERT: D 216 LYS cc_start: 0.1862 (ttpt) cc_final: 0.1451 (mttt) REVERT: D 304 LEU cc_start: 0.5180 (mt) cc_final: 0.4913 (pp) REVERT: D 305 TYR cc_start: 0.6251 (m-80) cc_final: 0.5994 (m-80) REVERT: D 349 TRP cc_start: 0.5613 (m-90) cc_final: 0.3228 (m-90) REVERT: D 398 ILE cc_start: 0.5034 (mm) cc_final: 0.4827 (mp) REVERT: E 116 ASN cc_start: 0.6341 (p0) cc_final: 0.5964 (m-40) REVERT: E 155 MET cc_start: 0.4842 (ptt) cc_final: 0.4105 (mtm) REVERT: E 372 PHE cc_start: 0.5690 (p90) cc_final: 0.5227 (p90) REVERT: E 734 VAL cc_start: 0.7268 (m) cc_final: 0.6977 (p) REVERT: F 49 THR cc_start: 0.3030 (p) cc_final: 0.2637 (t) REVERT: F 51 GLN cc_start: 0.6256 (tm-30) cc_final: 0.5807 (tt0) REVERT: F 85 PHE cc_start: 0.5846 (t80) cc_final: 0.5015 (t80) REVERT: F 184 MET cc_start: 0.5069 (tmt) cc_final: 0.4829 (tmm) REVERT: F 191 LYS cc_start: 0.4890 (ttpt) cc_final: 0.4626 (tppt) REVERT: F 242 GLU cc_start: 0.5032 (mp0) cc_final: 0.4432 (mm-30) REVERT: F 249 ARG cc_start: 0.5593 (mtt90) cc_final: 0.5270 (mmm-85) REVERT: F 260 ARG cc_start: 0.4283 (mtt90) cc_final: 0.2770 (ttp80) REVERT: F 407 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7598 (ptp-110) outliers start: 94 outliers final: 57 residues processed: 320 average time/residue: 0.1304 time to fit residues: 64.3305 Evaluate side-chains 281 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 748 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 713 PHE Chi-restraints excluded: chain E residue 719 PHE Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 102 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 180 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 193 HIS D 51 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS E 903 GLN F 368 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.222401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.151149 restraints weight = 29928.733| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.05 r_work: 0.3751 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18136 Z= 0.156 Angle : 0.701 12.039 24518 Z= 0.353 Chirality : 0.046 0.186 2838 Planarity : 0.005 0.048 3058 Dihedral : 5.806 48.574 2372 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.56 % Favored : 90.30 % Rotamer: Outliers : 3.57 % Allowed : 16.00 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.17), residues: 2144 helix: -0.38 (0.19), residues: 752 sheet: -2.07 (0.23), residues: 436 loop : -3.43 (0.17), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 331 TYR 0.018 0.001 TYR D 55 PHE 0.024 0.001 PHE F 401 TRP 0.016 0.001 TRP A 148 HIS 0.009 0.001 HIS F 460 Details of bonding type rmsd covalent geometry : bond 0.00358 (18136) covalent geometry : angle 0.70126 (24518) hydrogen bonds : bond 0.03735 ( 650) hydrogen bonds : angle 5.50180 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 249 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7834 (pt) REVERT: A 78 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7659 (pp) REVERT: A 216 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7438 (tptp) REVERT: A 271 THR cc_start: 0.7434 (OUTLIER) cc_final: 0.7095 (m) REVERT: B 117 PHE cc_start: 0.7345 (t80) cc_final: 0.7071 (t80) REVERT: B 363 LYS cc_start: 0.7416 (mmtp) cc_final: 0.7033 (tttp) REVERT: C 23 SER cc_start: 0.7914 (m) cc_final: 0.7713 (p) REVERT: C 64 ASN cc_start: 0.7587 (m110) cc_final: 0.6976 (m-40) REVERT: C 98 ILE cc_start: 0.7286 (mm) cc_final: 0.6775 (pt) REVERT: C 184 MET cc_start: 0.8756 (tmt) cc_final: 0.8265 (tmm) REVERT: C 191 LYS cc_start: 0.7633 (ttpt) cc_final: 0.7312 (tmtt) REVERT: C 414 LYS cc_start: 0.8337 (mmmt) cc_final: 0.8059 (mmtt) REVERT: D 216 LYS cc_start: 0.1958 (ttpt) cc_final: 0.1554 (mttt) REVERT: D 305 TYR cc_start: 0.6396 (m-80) cc_final: 0.6187 (m-80) REVERT: D 349 TRP cc_start: 0.5481 (m-90) cc_final: 0.3217 (m-90) REVERT: D 398 ILE cc_start: 0.5057 (mm) cc_final: 0.4848 (mt) REVERT: E 116 ASN cc_start: 0.6514 (p0) cc_final: 0.6117 (m-40) REVERT: E 155 MET cc_start: 0.4372 (ptt) cc_final: 0.3614 (mtm) REVERT: E 372 PHE cc_start: 0.5558 (p90) cc_final: 0.4946 (p90) REVERT: E 734 VAL cc_start: 0.7258 (m) cc_final: 0.6978 (p) REVERT: E 873 ASP cc_start: 0.4988 (t0) cc_final: 0.4762 (p0) REVERT: F 49 THR cc_start: 0.2767 (p) cc_final: 0.2386 (t) REVERT: F 51 GLN cc_start: 0.6435 (tm-30) cc_final: 0.6070 (tt0) REVERT: F 85 PHE cc_start: 0.5696 (t80) cc_final: 0.4692 (t80) REVERT: F 184 MET cc_start: 0.5220 (tmt) cc_final: 0.4998 (tmm) REVERT: F 242 GLU cc_start: 0.4864 (mp0) cc_final: 0.4233 (mm-30) REVERT: F 249 ARG cc_start: 0.5510 (mtt90) cc_final: 0.5085 (mmm-85) REVERT: F 260 ARG cc_start: 0.4600 (mtt90) cc_final: 0.3061 (ttp80) REVERT: F 265 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.4834 (mp) REVERT: F 316 LYS cc_start: 0.5592 (mttp) cc_final: 0.5350 (mmtm) REVERT: F 317 GLN cc_start: 0.7324 (tt0) cc_final: 0.6527 (tm-30) REVERT: F 407 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7845 (ptp-170) outliers start: 70 outliers final: 43 residues processed: 301 average time/residue: 0.1333 time to fit residues: 61.3893 Evaluate side-chains 262 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 872 HIS Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 372 HIS Chi-restraints excluded: chain F residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 141 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN B 100 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 ASN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS F 324 HIS F 460 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.218868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.149095 restraints weight = 30013.204| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.68 r_work: 0.3660 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18136 Z= 0.227 Angle : 0.778 16.210 24518 Z= 0.387 Chirality : 0.049 0.255 2838 Planarity : 0.005 0.054 3058 Dihedral : 5.866 48.030 2372 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.66 % Favored : 88.25 % Rotamer: Outliers : 4.79 % Allowed : 16.51 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.17), residues: 2144 helix: -0.40 (0.19), residues: 760 sheet: -2.15 (0.22), residues: 466 loop : -3.48 (0.17), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 373 TYR 0.017 0.002 TYR B 843 PHE 0.033 0.002 PHE F 219 TRP 0.016 0.002 TRP A 431 HIS 0.009 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00535 (18136) covalent geometry : angle 0.77776 (24518) hydrogen bonds : bond 0.04273 ( 650) hydrogen bonds : angle 5.56258 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 231 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8108 (pt) REVERT: A 78 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7763 (pp) REVERT: A 216 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7544 (tptp) REVERT: A 271 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7383 (m) REVERT: B 363 LYS cc_start: 0.7542 (mmtp) cc_final: 0.7180 (tttp) REVERT: C 64 ASN cc_start: 0.7764 (m110) cc_final: 0.7138 (m-40) REVERT: C 184 MET cc_start: 0.8758 (tmt) cc_final: 0.8313 (tmm) REVERT: C 191 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7384 (tttm) REVERT: C 321 CYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6153 (t) REVERT: C 372 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7080 (p-80) REVERT: C 414 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8029 (mmtt) REVERT: E 116 ASN cc_start: 0.6427 (p0) cc_final: 0.5871 (p0) REVERT: E 155 MET cc_start: 0.4321 (ptt) cc_final: 0.3675 (mtt) REVERT: E 719 PHE cc_start: 0.7120 (p90) cc_final: 0.6710 (p90) REVERT: E 734 VAL cc_start: 0.7245 (m) cc_final: 0.6956 (p) REVERT: E 762 LYS cc_start: 0.5336 (mmmm) cc_final: 0.4797 (ptpt) REVERT: E 782 LEU cc_start: 0.2151 (OUTLIER) cc_final: 0.1941 (pp) REVERT: E 857 LYS cc_start: 0.7278 (mmtt) cc_final: 0.7006 (mmmt) REVERT: F 184 MET cc_start: 0.5123 (tmt) cc_final: 0.4917 (tmm) REVERT: F 242 GLU cc_start: 0.5052 (mp0) cc_final: 0.4470 (mm-30) REVERT: F 249 ARG cc_start: 0.5679 (mtt90) cc_final: 0.5086 (mmm-85) REVERT: F 260 ARG cc_start: 0.4584 (mtt90) cc_final: 0.3263 (ttp80) REVERT: F 401 PHE cc_start: 0.7895 (t80) cc_final: 0.7687 (t80) REVERT: F 407 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7860 (ptp-170) outliers start: 94 outliers final: 65 residues processed: 298 average time/residue: 0.1357 time to fit residues: 61.6489 Evaluate side-chains 282 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 211 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 879 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 935 TYR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 372 HIS Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 133 optimal weight: 0.4980 chunk 181 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS F 324 HIS F 400 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.217693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150308 restraints weight = 29777.101| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.79 r_work: 0.3624 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18136 Z= 0.251 Angle : 0.787 13.142 24518 Z= 0.395 Chirality : 0.049 0.260 2838 Planarity : 0.005 0.048 3058 Dihedral : 5.950 48.071 2372 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.38 % Favored : 88.53 % Rotamer: Outliers : 4.99 % Allowed : 16.87 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.17), residues: 2144 helix: -0.47 (0.18), residues: 764 sheet: -2.11 (0.23), residues: 464 loop : -3.45 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 823 TYR 0.024 0.002 TYR B 822 PHE 0.021 0.002 PHE A 48 TRP 0.018 0.002 TRP A 148 HIS 0.023 0.002 HIS F 460 Details of bonding type rmsd covalent geometry : bond 0.00595 (18136) covalent geometry : angle 0.78689 (24518) hydrogen bonds : bond 0.04404 ( 650) hydrogen bonds : angle 5.62050 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 213 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8081 (pt) REVERT: A 78 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7792 (pp) REVERT: A 216 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7764 (tptp) REVERT: A 271 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7475 (m) REVERT: B 117 PHE cc_start: 0.7026 (t80) cc_final: 0.6700 (t80) REVERT: B 348 ASP cc_start: 0.5896 (OUTLIER) cc_final: 0.5431 (m-30) REVERT: B 363 LYS cc_start: 0.7568 (mmtp) cc_final: 0.7239 (tttp) REVERT: C 64 ASN cc_start: 0.7783 (m110) cc_final: 0.7150 (m-40) REVERT: C 98 ILE cc_start: 0.7309 (mm) cc_final: 0.6922 (pt) REVERT: C 184 MET cc_start: 0.8806 (tmt) cc_final: 0.8408 (tmm) REVERT: C 191 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7520 (tmtt) REVERT: C 321 CYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6190 (t) REVERT: C 372 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.6989 (p-80) REVERT: C 414 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8025 (mmtt) REVERT: D 216 LYS cc_start: 0.2206 (ttpt) cc_final: 0.1811 (mttt) REVERT: E 719 PHE cc_start: 0.7373 (p90) cc_final: 0.7110 (p90) REVERT: E 734 VAL cc_start: 0.7421 (m) cc_final: 0.7066 (p) REVERT: E 762 LYS cc_start: 0.5557 (mmmm) cc_final: 0.5033 (ptpt) REVERT: E 782 LEU cc_start: 0.2113 (OUTLIER) cc_final: 0.1890 (pp) REVERT: E 857 LYS cc_start: 0.7251 (mmtt) cc_final: 0.6959 (mmmt) REVERT: F 242 GLU cc_start: 0.5047 (mp0) cc_final: 0.4408 (mm-30) REVERT: F 249 ARG cc_start: 0.5692 (mtt90) cc_final: 0.4979 (mmm-85) REVERT: F 368 GLN cc_start: 0.4376 (OUTLIER) cc_final: 0.3845 (mp10) REVERT: F 391 LEU cc_start: 0.4307 (mp) cc_final: 0.4094 (mp) REVERT: F 401 PHE cc_start: 0.7843 (t80) cc_final: 0.7542 (t80) REVERT: F 407 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7809 (ptp-170) outliers start: 98 outliers final: 74 residues processed: 287 average time/residue: 0.1343 time to fit residues: 59.1473 Evaluate side-chains 280 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 198 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 726 SER Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 895 VAL Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 372 HIS Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 75 optimal weight: 0.0020 chunk 166 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 122 optimal weight: 0.0170 overall best weight: 0.5026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS D 125 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS F 64 ASN ** F 372 HIS ** 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 = 0.4790 r_free = 0.4790 target = 0.222335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.156376 restraints weight = 29915.509| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.45 r_work: 0.3726 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18136 Z= 0.123 Angle : 0.680 14.758 24518 Z= 0.338 Chirality : 0.045 0.227 2838 Planarity : 0.004 0.048 3058 Dihedral : 5.463 47.527 2372 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.65 % Favored : 90.25 % Rotamer: Outliers : 3.21 % Allowed : 18.81 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.17), residues: 2144 helix: 0.04 (0.19), residues: 754 sheet: -1.95 (0.22), residues: 482 loop : -3.25 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 436 TYR 0.019 0.001 TYR B 822 PHE 0.025 0.001 PHE C 295 TRP 0.019 0.001 TRP A 148 HIS 0.005 0.001 HIS F 65 Details of bonding type rmsd covalent geometry : bond 0.00273 (18136) covalent geometry : angle 0.67951 (24518) hydrogen bonds : bond 0.03490 ( 650) hydrogen bonds : angle 5.11094 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7698 (pt) REVERT: A 78 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7751 (pp) REVERT: A 216 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7576 (tptp) REVERT: B 348 ASP cc_start: 0.5815 (OUTLIER) cc_final: 0.5393 (m-30) REVERT: B 363 LYS cc_start: 0.7347 (mmtp) cc_final: 0.6981 (tttp) REVERT: C 64 ASN cc_start: 0.7620 (m110) cc_final: 0.6970 (m-40) REVERT: C 98 ILE cc_start: 0.7343 (mm) cc_final: 0.6773 (pt) REVERT: C 175 MET cc_start: 0.3336 (tmm) cc_final: 0.3117 (tmm) REVERT: C 184 MET cc_start: 0.8755 (tmt) cc_final: 0.8238 (tmm) REVERT: C 191 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7276 (tmtt) REVERT: C 372 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.6794 (p-80) REVERT: C 414 LYS cc_start: 0.8268 (mmmt) cc_final: 0.7948 (mmtt) REVERT: D 216 LYS cc_start: 0.2093 (ttpt) cc_final: 0.1626 (mttt) REVERT: D 288 HIS cc_start: 0.6907 (t70) cc_final: 0.6686 (t70) REVERT: D 319 LYS cc_start: 0.4901 (mppt) cc_final: 0.4153 (pptt) REVERT: D 339 SER cc_start: 0.3172 (OUTLIER) cc_final: 0.1315 (m) REVERT: D 349 TRP cc_start: 0.5445 (m-90) cc_final: 0.3098 (m-90) REVERT: E 155 MET cc_start: 0.3852 (ptt) cc_final: 0.3336 (mtt) REVERT: E 734 VAL cc_start: 0.7274 (m) cc_final: 0.6969 (p) REVERT: E 762 LYS cc_start: 0.5349 (mmmm) cc_final: 0.4830 (ptpt) REVERT: E 782 LEU cc_start: 0.2256 (OUTLIER) cc_final: 0.2026 (pp) REVERT: E 857 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6922 (mmmt) REVERT: E 861 TYR cc_start: 0.6463 (t80) cc_final: 0.6033 (t80) REVERT: F 51 GLN cc_start: 0.6267 (tm-30) cc_final: 0.6008 (tt0) REVERT: F 242 GLU cc_start: 0.4994 (mp0) cc_final: 0.4338 (mm-30) REVERT: F 249 ARG cc_start: 0.5562 (mtt90) cc_final: 0.4853 (mmm-85) REVERT: F 285 LYS cc_start: 0.7565 (pttt) cc_final: 0.7345 (ptmm) REVERT: F 317 GLN cc_start: 0.7279 (tt0) cc_final: 0.7051 (tt0) REVERT: F 401 PHE cc_start: 0.7852 (t80) cc_final: 0.7588 (t80) REVERT: F 427 PHE cc_start: 0.4591 (t80) cc_final: 0.4372 (t80) outliers start: 63 outliers final: 46 residues processed: 290 average time/residue: 0.1346 time to fit residues: 59.5777 Evaluate side-chains 271 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 372 HIS Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 115 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN C 207 ASN C 368 GLN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS E 868 HIS ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.220302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.150412 restraints weight = 29408.433| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.10 r_work: 0.3727 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18136 Z= 0.132 Angle : 0.677 14.931 24518 Z= 0.338 Chirality : 0.045 0.227 2838 Planarity : 0.004 0.045 3058 Dihedral : 5.321 47.479 2372 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.12 % Favored : 89.79 % Rotamer: Outliers : 3.47 % Allowed : 19.01 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.18), residues: 2144 helix: 0.09 (0.19), residues: 754 sheet: -1.78 (0.23), residues: 476 loop : -3.17 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 373 TYR 0.018 0.001 TYR B 822 PHE 0.014 0.001 PHE A 446 TRP 0.016 0.001 TRP A 148 HIS 0.005 0.001 HIS F 65 Details of bonding type rmsd covalent geometry : bond 0.00302 (18136) covalent geometry : angle 0.67712 (24518) hydrogen bonds : bond 0.03520 ( 650) hydrogen bonds : angle 5.00142 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7665 (pt) REVERT: A 78 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7737 (pp) REVERT: A 86 LYS cc_start: 0.9064 (ptpt) cc_final: 0.8836 (ptmm) REVERT: A 216 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7552 (tptp) REVERT: B 348 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.5346 (m-30) REVERT: B 363 LYS cc_start: 0.7297 (mmtp) cc_final: 0.6928 (tttp) REVERT: C 64 ASN cc_start: 0.7602 (m110) cc_final: 0.6902 (m-40) REVERT: C 98 ILE cc_start: 0.7275 (mm) cc_final: 0.6787 (pt) REVERT: C 175 MET cc_start: 0.3315 (tmm) cc_final: 0.3047 (tmm) REVERT: C 184 MET cc_start: 0.8688 (tmt) cc_final: 0.8202 (tmm) REVERT: C 191 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7251 (tmtt) REVERT: C 372 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.6781 (p-80) REVERT: C 414 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7941 (mmtt) REVERT: D 216 LYS cc_start: 0.2039 (ttpt) cc_final: 0.1589 (mttt) REVERT: D 288 HIS cc_start: 0.6939 (t70) cc_final: 0.6698 (t70) REVERT: D 339 SER cc_start: 0.3224 (OUTLIER) cc_final: 0.1394 (m) REVERT: D 349 TRP cc_start: 0.5385 (m-90) cc_final: 0.3043 (m-90) REVERT: E 734 VAL cc_start: 0.7275 (m) cc_final: 0.6995 (p) REVERT: E 762 LYS cc_start: 0.5358 (mmmm) cc_final: 0.4818 (ptpt) REVERT: E 782 LEU cc_start: 0.2280 (OUTLIER) cc_final: 0.2058 (pp) REVERT: E 803 TYR cc_start: 0.3919 (m-80) cc_final: 0.3714 (m-10) REVERT: E 861 TYR cc_start: 0.6765 (t80) cc_final: 0.6414 (t80) REVERT: E 878 GLU cc_start: 0.5529 (pp20) cc_final: 0.5136 (pp20) REVERT: E 888 LEU cc_start: 0.6112 (mm) cc_final: 0.5117 (mm) REVERT: F 51 GLN cc_start: 0.6294 (tm-30) cc_final: 0.6045 (tt0) REVERT: F 242 GLU cc_start: 0.4925 (mp0) cc_final: 0.4352 (mm-30) REVERT: F 249 ARG cc_start: 0.5559 (mtt90) cc_final: 0.5019 (mmm-85) REVERT: F 297 GLN cc_start: 0.5444 (pt0) cc_final: 0.4343 (tt0) REVERT: F 317 GLN cc_start: 0.7403 (tt0) cc_final: 0.7188 (tt0) REVERT: F 401 PHE cc_start: 0.7868 (t80) cc_final: 0.7590 (t80) REVERT: F 427 PHE cc_start: 0.4345 (t80) cc_final: 0.4134 (t80) outliers start: 68 outliers final: 50 residues processed: 276 average time/residue: 0.1303 time to fit residues: 55.8014 Evaluate side-chains 274 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 806 TYR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 72 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 GLN C 207 ASN C 368 GLN E 778 GLN E 846 HIS F 460 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.219010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.148554 restraints weight = 29587.738| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.44 r_work: 0.3692 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18136 Z= 0.170 Angle : 0.710 15.086 24518 Z= 0.354 Chirality : 0.046 0.269 2838 Planarity : 0.005 0.046 3058 Dihedral : 5.399 47.458 2372 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.19 % Favored : 88.71 % Rotamer: Outliers : 3.67 % Allowed : 19.32 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.18), residues: 2144 helix: -0.02 (0.19), residues: 770 sheet: -1.75 (0.23), residues: 474 loop : -3.18 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 373 TYR 0.020 0.002 TYR B 822 PHE 0.028 0.002 PHE E 719 TRP 0.017 0.001 TRP A 148 HIS 0.009 0.001 HIS F 460 Details of bonding type rmsd covalent geometry : bond 0.00403 (18136) covalent geometry : angle 0.70951 (24518) hydrogen bonds : bond 0.03728 ( 650) hydrogen bonds : angle 5.07732 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 219 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7889 (pt) REVERT: A 78 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7754 (pp) REVERT: A 147 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7678 (m) REVERT: A 216 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7608 (tptp) REVERT: B 95 MET cc_start: 0.4108 (ptm) cc_final: 0.3847 (tmm) REVERT: B 363 LYS cc_start: 0.7454 (mmtp) cc_final: 0.7070 (tttp) REVERT: C 64 ASN cc_start: 0.7770 (m110) cc_final: 0.7088 (m-40) REVERT: C 98 ILE cc_start: 0.7308 (mm) cc_final: 0.6849 (pt) REVERT: C 184 MET cc_start: 0.8701 (tmt) cc_final: 0.8219 (tmm) REVERT: C 191 LYS cc_start: 0.7717 (ttpt) cc_final: 0.7340 (tmtt) REVERT: C 321 CYS cc_start: 0.6319 (OUTLIER) cc_final: 0.6062 (t) REVERT: C 372 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.6804 (p-80) REVERT: C 414 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7985 (mmtt) REVERT: D 216 LYS cc_start: 0.1975 (ttpt) cc_final: 0.1532 (mttt) REVERT: D 288 HIS cc_start: 0.7017 (t70) cc_final: 0.6782 (t70) REVERT: D 339 SER cc_start: 0.3050 (OUTLIER) cc_final: 0.1055 (m) REVERT: D 349 TRP cc_start: 0.5262 (m-90) cc_final: 0.2905 (m-90) REVERT: E 155 MET cc_start: 0.4120 (ptt) cc_final: 0.3462 (mtt) REVERT: E 734 VAL cc_start: 0.7327 (m) cc_final: 0.7017 (p) REVERT: E 762 LYS cc_start: 0.5248 (mmmm) cc_final: 0.4831 (ptpt) REVERT: E 782 LEU cc_start: 0.2219 (OUTLIER) cc_final: 0.2017 (pp) REVERT: E 857 LYS cc_start: 0.7238 (mmtt) cc_final: 0.6919 (mmmt) REVERT: E 861 TYR cc_start: 0.6774 (t80) cc_final: 0.6438 (t80) REVERT: E 888 LEU cc_start: 0.6114 (mm) cc_final: 0.5084 (mm) REVERT: F 242 GLU cc_start: 0.4891 (mp0) cc_final: 0.4330 (mm-30) REVERT: F 249 ARG cc_start: 0.5661 (mtt90) cc_final: 0.5039 (mmm-85) REVERT: F 297 GLN cc_start: 0.5358 (pt0) cc_final: 0.4260 (tt0) REVERT: F 401 PHE cc_start: 0.7843 (t80) cc_final: 0.7555 (t80) REVERT: F 427 PHE cc_start: 0.4496 (t80) cc_final: 0.4107 (t80) REVERT: F 429 SER cc_start: 0.4148 (t) cc_final: 0.3073 (t) outliers start: 72 outliers final: 56 residues processed: 275 average time/residue: 0.1242 time to fit residues: 52.5943 Evaluate side-chains 272 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 782 LEU Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 45 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 163 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 GLN E 846 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.220857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153756 restraints weight = 29773.968| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.35 r_work: 0.3689 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18136 Z= 0.145 Angle : 0.689 15.527 24518 Z= 0.345 Chirality : 0.046 0.228 2838 Planarity : 0.004 0.046 3058 Dihedral : 5.319 47.429 2372 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.49 % Favored : 89.41 % Rotamer: Outliers : 3.36 % Allowed : 19.93 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.18), residues: 2144 helix: 0.11 (0.19), residues: 766 sheet: -1.68 (0.23), residues: 478 loop : -3.12 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 373 TYR 0.020 0.001 TYR B 822 PHE 0.015 0.001 PHE D 446 TRP 0.014 0.001 TRP A 148 HIS 0.007 0.001 HIS D 328 Details of bonding type rmsd covalent geometry : bond 0.00338 (18136) covalent geometry : angle 0.68897 (24518) hydrogen bonds : bond 0.03554 ( 650) hydrogen bonds : angle 4.97793 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 217 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7804 (pt) REVERT: A 78 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7742 (pp) REVERT: A 216 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7616 (tptp) REVERT: B 95 MET cc_start: 0.4153 (ptm) cc_final: 0.3916 (tmm) REVERT: B 363 LYS cc_start: 0.7461 (mmtp) cc_final: 0.7079 (tttp) REVERT: C 64 ASN cc_start: 0.7723 (m110) cc_final: 0.7031 (m-40) REVERT: C 98 ILE cc_start: 0.7283 (mm) cc_final: 0.6813 (pt) REVERT: C 184 MET cc_start: 0.8713 (tmt) cc_final: 0.8242 (tmm) REVERT: C 191 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7325 (tmtt) REVERT: C 321 CYS cc_start: 0.6268 (OUTLIER) cc_final: 0.6022 (t) REVERT: C 372 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.6725 (p-80) REVERT: C 414 LYS cc_start: 0.8309 (mmmt) cc_final: 0.7969 (mmtt) REVERT: D 216 LYS cc_start: 0.2181 (ttpt) cc_final: 0.1736 (mttt) REVERT: D 288 HIS cc_start: 0.7012 (t70) cc_final: 0.6759 (t70) REVERT: D 339 SER cc_start: 0.3043 (OUTLIER) cc_final: 0.1026 (m) REVERT: D 349 TRP cc_start: 0.5245 (m-90) cc_final: 0.2982 (m-90) REVERT: D 410 MET cc_start: 0.4630 (ptm) cc_final: 0.4024 (pmm) REVERT: E 155 MET cc_start: 0.4067 (ptt) cc_final: 0.3303 (mtt) REVERT: E 734 VAL cc_start: 0.7264 (m) cc_final: 0.6950 (p) REVERT: E 762 LYS cc_start: 0.5312 (mmmm) cc_final: 0.4891 (ptpt) REVERT: E 857 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6921 (mmmt) REVERT: E 861 TYR cc_start: 0.6505 (t80) cc_final: 0.6250 (t80) REVERT: F 120 GLU cc_start: 0.1035 (pm20) cc_final: 0.0606 (mt-10) REVERT: F 242 GLU cc_start: 0.4902 (mp0) cc_final: 0.4322 (mm-30) REVERT: F 249 ARG cc_start: 0.5549 (mtt90) cc_final: 0.5012 (mmm-85) REVERT: F 297 GLN cc_start: 0.5370 (pt0) cc_final: 0.4255 (tt0) REVERT: F 401 PHE cc_start: 0.7950 (t80) cc_final: 0.7657 (t80) REVERT: F 427 PHE cc_start: 0.4552 (t80) cc_final: 0.4203 (t80) REVERT: F 429 SER cc_start: 0.4778 (t) cc_final: 0.3791 (t) outliers start: 66 outliers final: 56 residues processed: 268 average time/residue: 0.1303 time to fit residues: 53.7093 Evaluate side-chains 269 residues out of total 1984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 118 TRP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 HIS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 435 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 339 SER Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 754 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 885 MET Chi-restraints excluded: chain E residue 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 318 MET Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 396 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 190 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 112 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN E 846 HIS E 912 HIS F 307 HIS F 328 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.218464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.148780 restraints weight = 29792.914| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.46 r_work: 0.3656 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18136 Z= 0.195 Angle : 0.743 15.615 24518 Z= 0.370 Chirality : 0.047 0.257 2838 Planarity : 0.005 0.049 3058 Dihedral : 5.486 47.464 2372 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.92 % Rotamer: Outliers : 3.92 % Allowed : 19.98 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.17), residues: 2144 helix: -0.06 (0.19), residues: 770 sheet: -1.74 (0.23), residues: 470 loop : -3.17 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 331 TYR 0.020 0.002 TYR B 822 PHE 0.028 0.002 PHE E 719 TRP 0.020 0.002 TRP A 148 HIS 0.007 0.001 HIS B 846 Details of bonding type rmsd covalent geometry : bond 0.00462 (18136) covalent geometry : angle 0.74305 (24518) hydrogen bonds : bond 0.03905 ( 650) hydrogen bonds : angle 5.12268 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6138.88 seconds wall clock time: 105 minutes 26.75 seconds (6326.75 seconds total)