Starting phenix.real_space_refine on Sat Sep 28 01:54:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/09_2024/6lt0_0966.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/09_2024/6lt0_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/09_2024/6lt0_0966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/09_2024/6lt0_0966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/09_2024/6lt0_0966.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lt0_0966/09_2024/6lt0_0966.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: {'GLN:plan1': 1, 'GLU:plan': 2, '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: 10.03, per 1000 atoms: 0.56 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: 4.05 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.25 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: 6.26 Time building geometry restraints manager: 4.78 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: 0.00 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 39.670 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- 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= 0.359 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 : 5.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.003 TRP A 118 HIS 0.013 0.002 HIS A 221 PHE 0.022 0.003 PHE F 99 TYR 0.025 0.002 TYR B 757 ARG 0.006 0.001 ARG D 56 *********************** 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 fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 1.925 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: 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: 0.5914 (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: 0.1751 (Cg_endo) REVERT: D 311 MET cc_start: 0.4390 (ttm) cc_final: 0.2802 (mmt) REVERT: E 155 MET cc_start: 0.4543 (ptt) cc_final: 0.4069 (mtp) REVERT: E 162 GLN cc_start: 0.5024 (tp-100) cc_final: 0.4588 (pm20) REVERT: E 888 LEU cc_start: 0.4505 (mp) cc_final: 0.4266 (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: 0.6141 (mt) REVERT: F 184 MET cc_start: 0.5608 (tmt) cc_final: 0.5308 (tmm) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.3593 time to fit residues: 252.6351 Evaluate side-chains 252 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 172 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 199 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 340 HIS E 366 HIS 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18136 Z= 0.230 Angle : 0.747 9.964 24518 Z= 0.379 Chirality : 0.047 0.184 2838 Planarity : 0.006 0.063 3058 Dihedral : 6.334 46.838 2372 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.91 % Favored : 88.99 % Rotamer: Outliers : 3.01 % Allowed : 11.88 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.16), residues: 2144 helix: -1.52 (0.16), residues: 748 sheet: -2.34 (0.23), residues: 436 loop : -3.80 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 148 HIS 0.014 0.001 HIS E 366 PHE 0.028 0.002 PHE C 61 TYR 0.019 0.002 TYR D 55 ARG 0.006 0.001 ARG F 394 *********************** 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 349 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 290 time to evaluate : 2.014 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: 0.7604 (m-10) cc_final: 0.6726 (m-90) REVERT: B 363 LYS cc_start: 0.7086 (mmtp) cc_final: 0.6725 (tttp) REVERT: C 64 ASN cc_start: 0.7307 (m110) cc_final: 0.6795 (m-40) REVERT: C 184 MET cc_start: 0.8502 (tmt) cc_final: 0.8026 (tmm) REVERT: C 191 LYS cc_start: 0.7302 (ttpt) cc_final: 0.6807 (tmtt) REVERT: C 298 VAL cc_start: 0.9178 (t) cc_final: 0.8746 (m) REVERT: C 334 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7066 (m) REVERT: C 414 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7703 (mmmt) REVERT: D 148 TRP cc_start: 0.1015 (t60) cc_final: 0.0654 (t60) REVERT: D 311 MET cc_start: 0.4315 (ttm) cc_final: 0.2879 (mmt) REVERT: E 116 ASN cc_start: 0.6094 (p0) cc_final: 0.5731 (m-40) REVERT: E 155 MET cc_start: 0.5032 (ptt) cc_final: 0.3973 (mtp) REVERT: F 49 THR cc_start: 0.3186 (p) cc_final: 0.2879 (t) REVERT: F 85 PHE cc_start: 0.3881 (t80) cc_final: 0.3319 (t80) REVERT: F 184 MET cc_start: 0.5182 (tmt) cc_final: 0.4879 (tmm) REVERT: F 318 MET cc_start: 0.6668 (mmm) cc_final: 0.6178 (ttm) outliers start: 59 outliers final: 36 residues processed: 334 average time/residue: 0.3119 time to fit residues: 158.8746 Evaluate side-chains 262 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 225 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 183 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 293 LEU 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 111 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 55 optimal weight: 0.0870 chunk 200 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 overall best weight: 4.0164 ------------------------------------------------------------------------------- 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 C 193 HIS D 83 HIS ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS F 64 ASN F 324 HIS F 328 GLN F 383 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6027 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 18136 Z= 0.484 Angle : 0.893 11.728 24518 Z= 0.451 Chirality : 0.053 0.293 2838 Planarity : 0.006 0.072 3058 Dihedral : 6.512 47.217 2372 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.50 % Favored : 87.36 % Rotamer: Outliers : 4.89 % Allowed : 14.12 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.16), residues: 2144 helix: -1.02 (0.18), residues: 734 sheet: -2.43 (0.22), residues: 456 loop : -3.60 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 148 HIS 0.027 0.003 HIS F 460 PHE 0.028 0.003 PHE C 427 TYR 0.031 0.003 TYR B 935 ARG 0.005 0.001 ARG D 302 *********************** 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 350 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 254 time to evaluate : 2.320 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: 0.8432 (OUTLIER) cc_final: 0.7923 (pt) REVERT: A 78 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7293 (pp) REVERT: B 363 LYS cc_start: 0.7189 (mmtp) cc_final: 0.6886 (tttp) REVERT: C 64 ASN cc_start: 0.7554 (m110) cc_final: 0.7008 (m-40) REVERT: C 184 MET cc_start: 0.8429 (tmt) cc_final: 0.7997 (tmm) REVERT: C 191 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7211 (tttm) REVERT: C 321 CYS cc_start: 0.6140 (OUTLIER) cc_final: 0.5886 (t) REVERT: C 327 ASN cc_start: 0.8209 (m-40) cc_final: 0.7966 (m110) REVERT: C 414 LYS cc_start: 0.8276 (mmmt) cc_final: 0.8004 (mmtt) REVERT: D 349 TRP cc_start: 0.2084 (m-90) cc_final: 0.1303 (m-90) REVERT: E 116 ASN cc_start: 0.6456 (p0) cc_final: 0.6086 (m-40) REVERT: E 155 MET cc_start: 0.4928 (ptt) cc_final: 0.3729 (mtm) REVERT: F 17 ILE cc_start: 0.3429 (OUTLIER) cc_final: 0.3180 (mp) REVERT: F 49 THR cc_start: 0.3227 (p) cc_final: 0.2897 (t) REVERT: F 51 GLN cc_start: 0.6093 (tm-30) cc_final: 0.5294 (tt0) REVERT: F 85 PHE cc_start: 0.4105 (t80) cc_final: 0.3450 (t80) REVERT: F 184 MET cc_start: 0.5325 (tmt) cc_final: 0.4928 (tmm) REVERT: F 242 GLU cc_start: 0.3037 (mp0) cc_final: 0.2307 (mm-30) outliers start: 96 outliers final: 62 residues processed: 325 average time/residue: 0.2807 time to fit residues: 139.7159 Evaluate side-chains 277 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 211 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 118 TRP 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 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 249 ASP 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 748 THR Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 888 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 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 183 VAL 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 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 321 CYS Chi-restraints excluded: chain C residue 371 LEU 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 713 PHE Chi-restraints excluded: chain E residue 719 PHE 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 17 ILE 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 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 197 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 134 optimal weight: 0.0070 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 30.0000 chunk 104 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5800 ------------------------------------------------------------------------------- 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 C 65 HIS D 51 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS E 708 GLN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS F 313 ASN F 324 HIS F 368 GLN ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18136 Z= 0.181 Angle : 0.698 14.539 24518 Z= 0.348 Chirality : 0.045 0.175 2838 Planarity : 0.004 0.047 3058 Dihedral : 5.810 46.952 2372 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.86 % Favored : 91.00 % Rotamer: Outliers : 2.80 % Allowed : 16.77 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.17), residues: 2144 helix: -0.41 (0.19), residues: 754 sheet: -2.06 (0.23), residues: 436 loop : -3.45 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 148 HIS 0.008 0.001 HIS F 460 PHE 0.025 0.001 PHE F 401 TYR 0.019 0.001 TYR E 822 ARG 0.005 0.000 ARG A 331 *********************** 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 305 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 250 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7428 (pt) REVERT: A 78 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7374 (pp) REVERT: B 363 LYS cc_start: 0.6767 (mmtp) cc_final: 0.6375 (tttp) REVERT: C 64 ASN cc_start: 0.7440 (m110) cc_final: 0.6849 (m-40) REVERT: C 98 ILE cc_start: 0.7236 (mm) cc_final: 0.6644 (pt) REVERT: C 184 MET cc_start: 0.8446 (tmt) cc_final: 0.7872 (tmm) REVERT: C 191 LYS cc_start: 0.7356 (ttpt) cc_final: 0.7004 (tmtt) REVERT: C 414 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7987 (mmtt) REVERT: D 349 TRP cc_start: 0.1816 (m-90) cc_final: 0.1221 (m-90) REVERT: E 155 MET cc_start: 0.4652 (ptt) cc_final: 0.3479 (mtm) REVERT: E 884 GLN cc_start: 0.5351 (pt0) cc_final: 0.4960 (mt0) REVERT: F 49 THR cc_start: 0.3011 (p) cc_final: 0.2722 (t) REVERT: F 51 GLN cc_start: 0.6153 (tm-30) cc_final: 0.5552 (tt0) REVERT: F 184 MET cc_start: 0.5319 (tmt) cc_final: 0.4971 (tmm) REVERT: F 242 GLU cc_start: 0.2576 (mp0) cc_final: 0.1974 (mm-30) outliers start: 55 outliers final: 32 residues processed: 289 average time/residue: 0.2958 time to fit residues: 129.3143 Evaluate side-chains 237 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP 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 249 ASP Chi-restraints excluded: chain B residue 349 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 183 VAL 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 D residue 52 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 713 PHE Chi-restraints excluded: chain E residue 726 SER 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 911 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 372 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 181 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- 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 ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18136 Z= 0.264 Angle : 0.716 12.357 24518 Z= 0.358 Chirality : 0.047 0.255 2838 Planarity : 0.005 0.050 3058 Dihedral : 5.700 46.465 2372 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.43 % Favored : 88.48 % Rotamer: Outliers : 3.62 % Allowed : 17.18 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 2144 helix: -0.32 (0.19), residues: 758 sheet: -2.11 (0.22), residues: 468 loop : -3.41 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 148 HIS 0.006 0.001 HIS F 460 PHE 0.039 0.002 PHE F 219 TYR 0.016 0.001 TYR B 935 ARG 0.009 0.000 ARG B 823 *********************** 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 290 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 219 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7541 (pt) REVERT: A 78 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7372 (pp) REVERT: B 117 PHE cc_start: 0.7398 (t80) cc_final: 0.6833 (t80) REVERT: B 363 LYS cc_start: 0.6876 (mmtp) cc_final: 0.6507 (tttp) REVERT: C 64 ASN cc_start: 0.7550 (m110) cc_final: 0.6944 (m-40) REVERT: C 98 ILE cc_start: 0.7190 (mm) cc_final: 0.6732 (pt) REVERT: C 184 MET cc_start: 0.8384 (tmt) cc_final: 0.7901 (tmm) REVERT: C 191 LYS cc_start: 0.7361 (ttpt) cc_final: 0.7021 (tmtt) REVERT: C 372 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.6932 (p-80) REVERT: C 414 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7901 (mmtt) REVERT: D 349 TRP cc_start: 0.1855 (m-90) cc_final: 0.1322 (m-90) REVERT: E 155 MET cc_start: 0.4813 (ptt) cc_final: 0.3464 (mtt) REVERT: F 184 MET cc_start: 0.5300 (tmt) cc_final: 0.4929 (tmm) REVERT: F 242 GLU cc_start: 0.2337 (mp0) cc_final: 0.1727 (mm-30) outliers start: 71 outliers final: 52 residues processed: 272 average time/residue: 0.2814 time to fit residues: 117.6051 Evaluate side-chains 249 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 194 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 174 THR 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 219 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 249 ASP 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 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 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 266 CYS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 372 HIS 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 323 ASP Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 398 ILE 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 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 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 440 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 71 optimal weight: 1.9990 chunk 191 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS B 100 GLN C 137 HIS C 297 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS E 868 HIS E 903 GLN F 324 HIS F 328 GLN ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18136 Z= 0.193 Angle : 0.676 13.226 24518 Z= 0.337 Chirality : 0.045 0.213 2838 Planarity : 0.004 0.044 3058 Dihedral : 5.491 46.489 2372 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.35 % Rotamer: Outliers : 3.62 % Allowed : 17.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.17), residues: 2144 helix: -0.17 (0.19), residues: 768 sheet: -1.80 (0.23), residues: 448 loop : -3.34 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 148 HIS 0.023 0.001 HIS F 460 PHE 0.034 0.001 PHE F 401 TYR 0.020 0.001 TYR B 822 ARG 0.006 0.000 ARG C 373 *********************** 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 291 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 220 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7421 (pt) REVERT: A 78 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7401 (pp) REVERT: B 117 PHE cc_start: 0.7294 (t80) cc_final: 0.6808 (t80) REVERT: B 363 LYS cc_start: 0.6760 (mmtp) cc_final: 0.6403 (tttp) REVERT: C 64 ASN cc_start: 0.7526 (m110) cc_final: 0.6913 (m-40) REVERT: C 98 ILE cc_start: 0.7191 (mm) cc_final: 0.6714 (pt) REVERT: C 184 MET cc_start: 0.8432 (tmt) cc_final: 0.7936 (tmm) REVERT: C 191 LYS cc_start: 0.7274 (ttpt) cc_final: 0.6913 (tmtt) REVERT: C 372 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6704 (p-80) REVERT: C 414 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7914 (mmtt) REVERT: D 349 TRP cc_start: 0.1683 (m-90) cc_final: 0.1240 (m-90) REVERT: E 155 MET cc_start: 0.4905 (ptt) cc_final: 0.3483 (mtt) REVERT: F 184 MET cc_start: 0.5299 (tmt) cc_final: 0.4906 (tmm) REVERT: F 242 GLU cc_start: 0.2834 (mp0) cc_final: 0.2135 (mm-30) outliers start: 71 outliers final: 51 residues processed: 271 average time/residue: 0.2825 time to fit residues: 117.9729 Evaluate side-chains 255 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 148 TRP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 LEU 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 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 144 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 288 THR 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 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 411 PHE Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 754 VAL 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 234 SER Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 372 HIS Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 212 optimal weight: 0.1980 chunk 132 optimal weight: 7.9990 chunk 129 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 297 GLN C 368 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 ASN ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS F 400 GLN F 460 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 18136 Z= 0.551 Angle : 0.897 13.065 24518 Z= 0.454 Chirality : 0.054 0.371 2838 Planarity : 0.006 0.063 3058 Dihedral : 6.268 45.580 2372 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.50 % Favored : 87.36 % Rotamer: Outliers : 4.33 % Allowed : 17.89 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.17), residues: 2144 helix: -0.71 (0.18), residues: 760 sheet: -2.06 (0.23), residues: 456 loop : -3.40 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP E 767 HIS 0.015 0.002 HIS B 846 PHE 0.037 0.003 PHE F 385 TYR 0.041 0.003 TYR A 305 ARG 0.009 0.001 ARG C 373 *********************** 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 280 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 195 time to evaluate : 1.947 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7886 (pt) REVERT: A 78 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7217 (pp) REVERT: A 164 LEU cc_start: 0.8548 (pp) cc_final: 0.8334 (tt) REVERT: B 363 LYS cc_start: 0.6973 (mmtp) cc_final: 0.6640 (tttp) REVERT: C 64 ASN cc_start: 0.7702 (m110) cc_final: 0.7068 (m-40) REVERT: C 184 MET cc_start: 0.8452 (tmt) cc_final: 0.8051 (tmm) REVERT: C 191 LYS cc_start: 0.7660 (ttpt) cc_final: 0.7388 (tmtt) REVERT: C 372 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7061 (p-80) REVERT: C 414 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7991 (mmtt) REVERT: D 339 SER cc_start: 0.2428 (OUTLIER) cc_final: 0.1821 (m) REVERT: D 349 TRP cc_start: 0.2019 (m-90) cc_final: 0.1176 (m-90) REVERT: E 103 PHE cc_start: 0.1991 (m-10) cc_final: 0.1286 (m-80) REVERT: E 924 MET cc_start: 0.4915 (tpp) cc_final: 0.4670 (tpt) REVERT: F 184 MET cc_start: 0.5658 (tmt) cc_final: 0.5173 (tmm) REVERT: F 242 GLU cc_start: 0.3024 (mp0) cc_final: 0.2236 (mm-30) REVERT: F 368 GLN cc_start: 0.5003 (OUTLIER) cc_final: 0.4433 (mp10) outliers start: 85 outliers final: 69 residues processed: 262 average time/residue: 0.2682 time to fit residues: 109.7366 Evaluate side-chains 254 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 180 time to evaluate : 2.182 ------------------------------------------------------------------------------- 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 174 THR 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 249 ASP 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 84 THR 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 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 144 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 195 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 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 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 315 ILE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 339 SER 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 165 ILE Chi-restraints excluded: chain E residue 726 SER Chi-restraints excluded: chain E residue 734 VAL 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 265 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 372 HIS Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 104 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 272 GLN B 100 GLN ** B 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS C 368 GLN ** 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 ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18136 Z= 0.340 Angle : 0.758 14.039 24518 Z= 0.383 Chirality : 0.049 0.297 2838 Planarity : 0.005 0.051 3058 Dihedral : 5.934 45.630 2372 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.54 % Favored : 89.37 % Rotamer: Outliers : 4.13 % Allowed : 18.71 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.17), residues: 2144 helix: -0.46 (0.18), residues: 758 sheet: -1.99 (0.23), residues: 458 loop : -3.28 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 767 HIS 0.008 0.001 HIS B 846 PHE 0.039 0.002 PHE F 385 TYR 0.023 0.002 TYR B 822 ARG 0.007 0.001 ARG C 373 *********************** 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 274 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 193 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7741 (pt) REVERT: A 164 LEU cc_start: 0.8500 (pp) cc_final: 0.8178 (tt) REVERT: B 363 LYS cc_start: 0.6876 (mmtp) cc_final: 0.6527 (tttp) REVERT: C 64 ASN cc_start: 0.7702 (m110) cc_final: 0.7058 (m-40) REVERT: C 98 ILE cc_start: 0.7317 (mm) cc_final: 0.6858 (pt) REVERT: C 184 MET cc_start: 0.8473 (tmt) cc_final: 0.8077 (tmm) REVERT: C 191 LYS cc_start: 0.7548 (ttpt) cc_final: 0.7246 (tmtt) REVERT: C 334 SER cc_start: 0.7349 (OUTLIER) cc_final: 0.7020 (m) REVERT: C 372 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.6551 (p-80) REVERT: C 414 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7979 (mmtt) REVERT: D 339 SER cc_start: 0.2387 (OUTLIER) cc_final: 0.1556 (m) REVERT: D 349 TRP cc_start: 0.1948 (m-90) cc_final: 0.1256 (m-90) REVERT: E 155 MET cc_start: 0.4097 (ptt) cc_final: 0.3485 (mtm) REVERT: F 184 MET cc_start: 0.5554 (tmt) cc_final: 0.5097 (tmm) REVERT: F 242 GLU cc_start: 0.2987 (mp0) cc_final: 0.2199 (mm-30) outliers start: 81 outliers final: 66 residues processed: 253 average time/residue: 0.2736 time to fit residues: 108.7731 Evaluate side-chains 251 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 181 time to evaluate : 2.181 ------------------------------------------------------------------------------- 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 67 VAL 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 174 THR 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 249 ASP Chi-restraints excluded: chain A residue 296 VAL 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 746 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 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 187 LEU Chi-restraints excluded: chain C residue 195 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 334 SER 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 384 VAL 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 339 SER 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 165 ILE Chi-restraints excluded: chain E residue 734 VAL Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 866 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 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 265 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 372 HIS Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 437 LEU Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.2582 ------------------------------------------------------------------------------- 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 C 137 HIS C 368 GLN ** 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 814 ASN E 846 HIS ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS F 324 HIS ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.6207 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= 0.302 Angle : 0.747 14.433 24518 Z= 0.375 Chirality : 0.048 0.261 2838 Planarity : 0.005 0.049 3058 Dihedral : 5.793 46.006 2372 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.71 % Favored : 88.20 % Rotamer: Outliers : 4.18 % Allowed : 18.96 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.17), residues: 2144 helix: -0.37 (0.19), residues: 762 sheet: -1.92 (0.23), residues: 464 loop : -3.24 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 767 HIS 0.008 0.001 HIS F 460 PHE 0.034 0.002 PHE F 385 TYR 0.022 0.002 TYR B 822 ARG 0.008 0.000 ARG C 373 *********************** 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 277 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 195 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7718 (pt) REVERT: A 49 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8149 (mp) REVERT: A 164 LEU cc_start: 0.8487 (pp) cc_final: 0.8144 (tt) REVERT: B 363 LYS cc_start: 0.6891 (mmtp) cc_final: 0.6538 (tttp) REVERT: C 64 ASN cc_start: 0.7865 (m-40) cc_final: 0.7161 (m-40) REVERT: C 98 ILE cc_start: 0.7314 (mm) cc_final: 0.6853 (pt) REVERT: C 184 MET cc_start: 0.8504 (tmt) cc_final: 0.8100 (tmm) REVERT: C 191 LYS cc_start: 0.7508 (ttpt) cc_final: 0.7208 (tmtt) REVERT: C 334 SER cc_start: 0.7090 (OUTLIER) cc_final: 0.6883 (m) REVERT: C 372 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6613 (p-80) REVERT: C 414 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7980 (mmtt) REVERT: D 339 SER cc_start: 0.2448 (OUTLIER) cc_final: 0.1566 (m) REVERT: D 349 TRP cc_start: 0.1985 (m-90) cc_final: 0.1424 (m-90) REVERT: E 924 MET cc_start: 0.3802 (tpp) cc_final: 0.3134 (tpt) REVERT: F 184 MET cc_start: 0.5568 (tmt) cc_final: 0.5088 (tmm) REVERT: F 242 GLU cc_start: 0.3126 (mp0) cc_final: 0.2324 (mm-30) outliers start: 82 outliers final: 64 residues processed: 260 average time/residue: 0.2777 time to fit residues: 111.9045 Evaluate side-chains 254 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 185 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 67 VAL 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 174 THR 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 249 ASP 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 746 LEU Chi-restraints excluded: chain B residue 806 TYR Chi-restraints excluded: chain B residue 835 THR 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 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 187 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 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 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 384 VAL 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 315 ILE Chi-restraints excluded: chain D residue 339 SER 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 165 ILE Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 894 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 368 GLN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain F residue 460 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 99 optimal weight: 1.9990 chunk 145 optimal weight: 0.0070 chunk 219 optimal weight: 10.0000 chunk 201 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 137 HIS C 368 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS F 460 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18136 Z= 0.259 Angle : 0.723 14.910 24518 Z= 0.363 Chirality : 0.047 0.218 2838 Planarity : 0.005 0.049 3058 Dihedral : 5.646 46.088 2372 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.17 % Favored : 89.74 % Rotamer: Outliers : 3.67 % Allowed : 19.88 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.17), residues: 2144 helix: -0.25 (0.19), residues: 770 sheet: -1.81 (0.23), residues: 460 loop : -3.20 (0.18), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 767 HIS 0.007 0.001 HIS F 372 PHE 0.030 0.002 PHE F 385 TYR 0.021 0.002 TYR B 822 ARG 0.009 0.000 ARG F 129 ********************** 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 263 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 191 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7552 (pt) REVERT: A 49 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 164 LEU cc_start: 0.8450 (pp) cc_final: 0.8079 (tt) REVERT: B 363 LYS cc_start: 0.6901 (mmtp) cc_final: 0.6572 (tttp) REVERT: C 64 ASN cc_start: 0.7890 (m-40) cc_final: 0.7188 (m-40) REVERT: C 98 ILE cc_start: 0.7286 (mm) cc_final: 0.6834 (pt) REVERT: C 184 MET cc_start: 0.8514 (tmt) cc_final: 0.8091 (tmm) REVERT: C 191 LYS cc_start: 0.7494 (ttpt) cc_final: 0.7174 (tmtt) REVERT: C 372 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6503 (p-80) REVERT: C 414 LYS cc_start: 0.8226 (mmmt) cc_final: 0.7893 (mmtt) REVERT: D 339 SER cc_start: 0.2689 (OUTLIER) cc_final: 0.1848 (m) REVERT: D 349 TRP cc_start: 0.1882 (m-90) cc_final: 0.1433 (m-90) REVERT: E 155 MET cc_start: 0.4434 (ptt) cc_final: 0.3904 (ttt) REVERT: E 878 GLU cc_start: 0.5933 (pp20) cc_final: 0.5676 (pp20) REVERT: F 184 MET cc_start: 0.5674 (tmt) cc_final: 0.5203 (tmm) REVERT: F 242 GLU cc_start: 0.3237 (mp0) cc_final: 0.2439 (mm-30) outliers start: 72 outliers final: 62 residues processed: 248 average time/residue: 0.2806 time to fit residues: 108.0314 Evaluate side-chains 242 residues out of total 1984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 176 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 67 VAL 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 174 THR 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 249 ASP 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 746 LEU Chi-restraints excluded: chain B residue 806 TYR Chi-restraints excluded: chain B residue 835 THR 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 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 187 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 201 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 372 HIS Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 384 VAL 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 339 SER Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 433 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 841 SER Chi-restraints excluded: chain E residue 866 HIS Chi-restraints excluded: chain E residue 894 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 263 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 368 GLN Chi-restraints excluded: chain F residue 375 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 137 HIS ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 HIS ** E 884 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 HIS F 216 HIS F 307 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.215843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147903 restraints weight = 29217.836| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.35 r_work: 0.3633 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18136 Z= 0.317 Angle : 0.752 15.116 24518 Z= 0.378 Chirality : 0.048 0.326 2838 Planarity : 0.005 0.053 3058 Dihedral : 5.727 46.362 2372 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.89 % Favored : 88.01 % Rotamer: Outliers : 3.92 % Allowed : 19.88 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.17), residues: 2144 helix: -0.24 (0.19), residues: 760 sheet: -1.81 (0.23), residues: 474 loop : -3.21 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 767 HIS 0.009 0.001 HIS F 460 PHE 0.026 0.002 PHE C 295 TYR 0.022 0.002 TYR B 822 ARG 0.006 0.000 ARG C 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3967.50 seconds wall clock time: 71 minutes 35.16 seconds (4295.16 seconds total)